Align glycolaldehyde oxidoreductase medium subunit (characterized)
to candidate BPHYT_RS10830 BPHYT_RS10830 carbon monoxide dehydrogenase
Query= metacyc::MONOMER-18072 (282 letters) >FitnessBrowser__BFirm:BPHYT_RS10830 Length = 273 Score = 135 bits (341), Expect = 8e-37 Identities = 92/283 (32%), Positives = 149/283 (52%), Gaps = 16/283 (5%) Query: 1 MYPPDFTYVRVSSSEEATKFL-ESHDDARPLAGGQSLIPMLKLRVISPNYIVDLNPITSL 59 M P F Y+R +++ A L +S +DAR LAGGQSL+ +L +R+ P ++D++ L Sbjct: 1 MKPAPFDYLRAMTTQHALDALAQSGEDARVLAGGQSLMAVLNMRLAQPRVLIDISRTDEL 60 Query: 60 SYVRSSFNS--TKIGALTRYNEILKNDLVRVNVPLLHQAVRVVGDMQVRNLGTIGGSAAN 117 VR + +GA + + +R VPLL A + Q+RN GT+ GS A+ Sbjct: 61 GSVRVDHKAGLLTVGAAATQGNVEWRETLRDEVPLLAMAFPHISHFQIRNRGTVCGSVAH 120 Query: 118 ADPSADIPTVLTALNAEIILSSASGNRSVNALDFFKGAFATDLRKGEIISEIVLP-NLEG 176 ADPSA++P VL AL +++L S +R + A +FF+G T E++ + P G Sbjct: 121 ADPSAELPLVLAALGGDVMLRSRKKHRVLPAGEFFQGMLMTAREPDELVEAVRFPLKRPG 180 Query: 177 YRTIYKKVVRRAGDFALVSLALAIKLRQNEIEDIRLAYGGVGERPFRALEVEKSVMGKRL 236 R + + R GDFA+V+ A + + IRLA GGV +RP VE+ RL Sbjct: 181 ERYGFTEFSARHGDFAMVACAAVV-----TSDSIRLAVGGVADRPV----VEQ---WPRL 228 Query: 237 NDELVEEIVSKVSSQVNPPSDTRGSSWYRREVMKVITRKALKE 279 DE + ++ +S ++ D S+ YRR +++ + + ++E Sbjct: 229 RDEDLRGALNDLSWKLGAQDDAHISAAYRRHLVRQLGWRVIEE 271 Lambda K H 0.317 0.134 0.367 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: 166 Number of extensions: 5 Number of successful extensions: 4 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: 282 Length of database: 273 Length adjustment: 25 Effective length of query: 257 Effective length of database: 248 Effective search space: 63736 Effective search space used: 63736 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 47 (22.7 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