Align D-lactate oxidase and glycolate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate RR42_RS17285 RR42_RS17285 2-hydroxy-acid oxidase
Query= reanno::psRCH2:GFF3772 (499 letters) >FitnessBrowser__Cup4G11:RR42_RS17285 Length = 472 Score = 225 bits (573), Expect = 3e-63 Identities = 141/415 (33%), Positives = 208/415 (50%), Gaps = 7/415 (1%) Query: 59 VVLPERIEQVETLLKLCHQRGVPVVARGAGTGLSGGALPLEQGILLVMARFNKILEVDPA 118 VV E+V + +LC++ VP++A GAG+ L G L + GI L ++ NK+L V P Sbjct: 56 VVFAHTTEEVAEVARLCNEHRVPLIAYGAGSSLEGHLLAVAGGISLDLSEMNKVLSVQPE 115 Query: 119 GRFARVQPGVRNLAISQAAAPYELYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHN 178 VQPGV ++Q L++ DP + S+GG A A G + ++YG N Sbjct: 116 DLNVTVQPGVTRKQLNQEIKDSGLFFPIDPGAD--ASLGGMCATRASGTNAVRYGTMREN 173 Query: 179 LLKVDILTVEGERMTLGSDAL-DSPGFDLLALFTGSEGMLGIVTEVTVKLLPKPQVAKVL 237 +L + ++T +G + G+ A S G+DL L GSEG LGI+TEVTV+L P+P+ Sbjct: 174 VLALTVVTADGRIIKTGTHARKSSAGYDLTRLMIGSEGTLGIITEVTVRLYPQPEAISAA 233 Query: 238 LAAFDSVEKAGRAVGDIIAAGIIPGGLEMMDNLSIRAAEDFIHAGYPVDAEAILLCELDG 297 + +F S+ A RA + I G+ +E +D L+IRA H + L E G Sbjct: 234 ICSFPSMGSAVRATIETIQLGVPVARVEFVDALAIRAINR--HDNLSMPEAPHLFFEFHG 291 Query: 298 VEADVHDDCARVSEVLKLAGATEVRLAKDEAERVRFWAGRKNAFPAVGRISPDYYCM--D 355 EA V + V ++ G A +R R W R A+ A+ ++ P + D Sbjct: 292 TEAGVKEQAETVQQIAADNGGQGFEWATRPEDRSRLWNARHTAYFAMLQLKPGCKAVTTD 351 Query: 356 GTIPRRELPGVLKGISDLSEQFGLRVANVFHAGDGNMHPLILFDANQPGELERAEDLGGK 415 +P L + L V H GDGN H IL D +P EL AE + + Sbjct: 352 VCVPISRLADCVTETERDLNASSLPCPIVGHVGDGNFHVAILTDPEKPEELAEAETINRR 411 Query: 416 ILELCVKVGGSITGEHGVGREKINQMCSQFNADELTLFHAVKAAFDPSGLLNPGK 470 I+E + +GG+ TGEHGVG K++ + S+ D L L A+K A DP+ +LNPGK Sbjct: 412 IVERALAMGGTCTGEHGVGLHKMDFLVSEHGEDALDLMRAIKNALDPNHILNPGK 466 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: 537 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: 472 Length adjustment: 34 Effective length of query: 465 Effective length of database: 438 Effective search space: 203670 Effective search space used: 203670 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