Align D-lactate oxidase and glycolate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate H281DRAFT_02585 H281DRAFT_02585 FAD/FMN-containing dehydrogenase
Query= reanno::psRCH2:GFF3772 (499 letters) >FitnessBrowser__Burk376:H281DRAFT_02585 Length = 461 Score = 166 bits (421), Expect = 1e-45 Identities = 139/471 (29%), Positives = 225/471 (47%), Gaps = 40/471 (8%) Query: 20 ALLAELQAQLPDLDILHRSEDLKPYECDGLSAYRTTPLLVVLPERIEQVETLLKLCHQRG 79 ALLAEL A + L S L+ + GL P ++ P E V L++CH Sbjct: 9 ALLAELGADVVQLPAEFGSRKLQDWS--GLPG--AVPTALIRPRSTEDVARALRVCHAFS 64 Query: 80 VPVVARGAGTGLSGGALPLEQGILLVMARFNKILEVDPAGRFARVQPGVRNLAISQAAAP 139 PVV +G TGL GGA L + L + R N+I+EVD V+ GV + +AA Sbjct: 65 QPVVTQGGLTGLVGGANALGGEVALSLERMNRIVEVDRTSATMTVEAGVPLQVVQEAALD 124 Query: 140 YELYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLLKVDILTVEGERMTLGSDAL 199 Y+ D ++ +C+IGGN+A NAGG +KYG+ +L ++ + GE +T G + Sbjct: 125 AGFYFPLDLGARGSCTIGGNLATNAGGNRVIKYGMMRDQVLGIEAVLANGE-VTSGMHKM 183 Query: 200 --DSPGFDLLALFTGSEGMLGIVTEVTVKLLPKP---QVAKVLLAAFDSVEK-------- 246 ++ G+DL L GSEG L ++T ++L P+P A L +D+V K Sbjct: 184 IKNNSGYDLRHLLIGSEGTLAVITRAVLRLRPRPTAVATAWCALPDYDAVTKLLACSQAQ 243 Query: 247 --AGRAVGDIIAAGIIPGGLEMMDNLSIRAAEDFIHAGYPVDAEAILLCELDGVEADVHD 304 AG + +++ AG ++ NL +RA D + Y +L E G + D H Sbjct: 244 LSAGVSAFEVMWAGYYDA---VLANLPLRAPLDKHYPYY-------VLLESVGSDPDRHA 293 Query: 305 DC--ARVSEVLKLAGATEVRLAKDEAERVRFWAGRKNAFPAVGRISPDYYCMDGTIPRRE 362 + A + ++L+ ++ LA+ EA+ FW R +A + P + D + + Sbjct: 294 EAFEAFLGDMLEAGVVSDAALAQSEADAQAFWTIR-DAPGEYPKFIPHHSAYDVSFSISD 352 Query: 363 LPGVLKGISD-LSEQFGLRVANVF-HAGDGNMHPLILFDANQPGELERAED-LGGKILEL 419 + V L E++ + ++ H GDGN+H ++ + PG R D + I ++ Sbjct: 353 VGQVAAHCEQRLQERWPDALVMIYGHLGDGNLHIVV----DIPGSEGRLHDEIDRVIYDV 408 Query: 420 CVKVGGSITGEHGVGREKINQMCSQFNADELTLFHAVKAAFDPSGLLNPGK 470 + GS++ EHG+G +K + + E+T +K A DP +LNPGK Sbjct: 409 TREFHGSVSAEHGIGVKKKAYLGHTRSDAEITAMRLIKTALDPRSILNPGK 459 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: 531 Number of extensions: 29 Number of successful extensions: 5 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: 461 Length adjustment: 34 Effective length of query: 465 Effective length of database: 427 Effective search space: 198555 Effective search space used: 198555 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 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