Align D-lactate oxidase and glycolate oxidase, iron-sulfur subunit (EC 1.1.3.15) (characterized)
to candidate Pf1N1B4_5864 Glycolate dehydrogenase (EC 1.1.99.14), iron-sulfur subunit GlcF
Query= reanno::psRCH2:GFF3770 (405 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5864 Length = 405 Score = 617 bits (1590), Expect = 0.0 Identities = 294/405 (72%), Positives = 337/405 (83%) Query: 1 MQTNLSEAAKKLPRAEEAESILRSCVHCGFCNATCPTYQLLGDELDGPRGRIYLMKQMFE 60 MQTNLSE +K LPRAEEA+ ILR+CVHCGFCNATCPTYQLLGDELDGPRGRIYL+KQ+ E Sbjct: 1 MQTNLSEQSKLLPRAEEADKILRTCVHCGFCNATCPTYQLLGDELDGPRGRIYLIKQVLE 60 Query: 61 GGEVTESTQLHLDRCLTCRNCETTCPSGVKYHNLLDIGRDFIEQQVQRPLGERVVRGGLR 120 G T QLHLDRCLTCRNCETTCPSGV YHNLLDIGR I+Q V RP +R++R GLR Sbjct: 61 GAPATAKAQLHLDRCLTCRNCETTCPSGVDYHNLLDIGRAVIDQAVPRPASQRLLRQGLR 120 Query: 121 TVIPRPGLFKALLGAGNALKPLMPASLKDHLPREIRPAKPRPQVMHSRRVLILEGCVQPS 180 + P P LFK LL G +PL+P ++ LP ++ A RP H+RRVL+LEGCVQP Sbjct: 121 ALAPNPNLFKTLLQIGATFRPLLPRGIEAKLPHDLPAAGERPAPRHARRVLMLEGCVQPG 180 Query: 181 LSPSTNAAAARVLDRLGISVSPAREAGCCGAVDYHLNAQDAGLDRARRNIDAWWPAIEAG 240 LSP+TNAA ARVLDRLGISV PA EAGCCGA+DYHL+AQ GLDRARRNIDAWWP +E G Sbjct: 181 LSPNTNAATARVLDRLGISVIPAPEAGCCGALDYHLDAQAMGLDRARRNIDAWWPHLENG 240 Query: 241 AEAIVQTASGCGAFVKEYGHLLKDDPAYAAKAARVSELAKDLVEVLRSAELEKLNVRADK 300 AEAIVQTASGCGAF+K+YGHLL+ DP YAAKA RVSELA DLV+VL LE++ D+ Sbjct: 241 AEAIVQTASGCGAFIKDYGHLLERDPVYAAKAQRVSELALDLVQVLADEPLERVCTATDQ 300 Query: 301 RMAFHCPCTLQHAQKLGGAVEDVLTRLGYQLTAVPDAHLCCGSAGSYSITQPEISHQLRD 360 R+AFHCPCTLQHAQKLGGAVE VLTRLG+ LTAVPD+HLCCGSAG+YSITQP ++ QLRD Sbjct: 301 RIAFHCPCTLQHAQKLGGAVEAVLTRLGFNLTAVPDSHLCCGSAGTYSITQPVLARQLRD 360 Query: 361 NKLNALESGKPEVIVTANIGCQTHLDGAGRTPVKHWIEVVEESMQ 405 NKLNALESG PEVI TANIGCQ+HL+ AGRTPV+HWIE+V++ ++ Sbjct: 361 NKLNALESGHPEVIATANIGCQSHLNSAGRTPVRHWIELVDQVLR 405 Lambda K H 0.319 0.135 0.410 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: 653 Number of extensions: 19 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: 405 Length of database: 405 Length adjustment: 31 Effective length of query: 374 Effective length of database: 374 Effective search space: 139876 Effective search space used: 139876 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: 50 (23.9 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