Align D-lactate oxidase and glycolate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate Pf6N2E2_136 Glycolate dehydrogenase (EC 1.1.99.14), FAD-binding subunit GlcE
Query= reanno::psRCH2:GFF3771 (353 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_136 Length = 352 Score = 505 bits (1301), Expect = e-148 Identities = 251/347 (72%), Positives = 285/347 (82%), Gaps = 2/347 (0%) Query: 7 DASAQLLDQVNQALAANTPLRIQGSGSKSFLGLQADGVLLDTREHRGIVSYDPTELVVTV 66 DAS LL+QVN+A A TPLRIQGS SK+FLG + G +LDTR HRGIV YDPTELV+T Sbjct: 8 DASDLLLEQVNRARANATPLRIQGSNSKAFLGREVAGEVLDTRVHRGIVHYDPTELVITA 67 Query: 67 RAGTPLTELETALDEAGQMLPCEPPHFGEGATVGGMIAAGLSGPRRPWSGSVRDFVLGSR 126 RAGTPL EL ALD AGQ LPCEPP FG+ ATVGGM+AAGLSGPRRPW+GSVRDFVLG+R Sbjct: 68 RAGTPLLELLAALDAAGQRLPCEPPAFGDDATVGGMVAAGLSGPRRPWAGSVRDFVLGTR 127 Query: 127 VITGQGKHLRFGGEVMKNVAGYDLSRLMAGSFGCLGVLTEVSLKVLPKPRLCTSLRLEID 186 +I+G G LRFGGEVMKNVAGYDLSRL+AGSFGCLGV+TEVSLKVLPKPR S+RLE+D Sbjct: 128 LISGHGTLLRFGGEVMKNVAGYDLSRLLAGSFGCLGVITEVSLKVLPKPRHSLSIRLELD 187 Query: 187 LERALLKLAEWGQQPIPISAASHDGQALHLRLEGGEGSVGAARERIGGEDLDPGYWNDLR 246 AL KLAEWG+QP+PISAASHDG LHLRLEGGEGSV AA +R GGE +D YW L Sbjct: 188 STEALGKLAEWGRQPLPISAASHDGDCLHLRLEGGEGSVSAAHQRFGGEVIDDQYWTALN 247 Query: 247 EQRLAFFADPRPLWRLSLPNNTPALGLPGDQLVDWAGAQRWLKSDADAVTIRGIAIEVGG 306 E +LAFF + PLWRLSLPN+T L LPG QL+DWAGAQRW+K++AD T++ +A EVGG Sbjct: 248 EHQLAFFDEGLPLWRLSLPNHTGPLTLPGAQLIDWAGAQRWVKTEAD--TVQALAHEVGG 305 Query: 307 HATCFTAGATTNPFQPLAAPLLRYHRQLKAALDPQGIFNPGRMYSEV 353 HATC+ GA+ PFQPLA LLRYHRQLKA LDP G+FNPGRMY E+ Sbjct: 306 HATCYRQGASDTPFQPLAPALLRYHRQLKAQLDPLGLFNPGRMYPEL 352 Lambda K H 0.319 0.137 0.417 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: 505 Number of extensions: 15 Number of successful extensions: 2 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: 353 Length of database: 352 Length adjustment: 29 Effective length of query: 324 Effective length of database: 323 Effective search space: 104652 Effective search space used: 104652 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 (21.7 bits) S2: 49 (23.5 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