Align glycolaldehyde oxidoreductase medium subunit (characterized)
to candidate AO356_26660 AO356_26660 carbon monoxide dehydrogenase
Query= metacyc::MONOMER-18072 (282 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_26660 Length = 268 Score = 159 bits (401), Expect = 8e-44 Identities = 97/282 (34%), Positives = 151/282 (53%), Gaps = 16/282 (5%) Query: 1 MYPPDFTYVRVSSSEEATKFLESH-DDARPLAGGQSLIPMLKLRVISPNYIVDLNPITSL 59 M P F YVR + + + L + +AR +AGGQSL+ +L +R+ P ++D+N + L Sbjct: 1 MKPAAFDYVRADTRRQVVELLAEYGQEARIIAGGQSLMAVLNMRLAQPKLLIDINHVAEL 60 Query: 60 SYVRSSFNSTKIGALTRYNEILKNDLVRVNVPLLHQAVRVVGDMQVRNLGTIGGSAANAD 119 +Y+ + +GA R ++L + VPLL A+ +G Q RN GT+ GS A+AD Sbjct: 61 AYIELRKDCLAVGAGVRQAQLLARSTLMDEVPLLALAMPWIGHFQTRNRGTVCGSVAHAD 120 Query: 120 PSADIPTVLTALNAEIILSSASGNRSVNALDFFKGAFATDLRKGEIISEIVLP-NLEGYR 178 PSA++P L L EI+L S G R V A DFF+G TD R E++ E+ P EG Sbjct: 121 PSAELPLCLVTLGGEIVLESKKGKRIVKAADFFQGILTTDKRADELVVEVRFPLKREGIT 180 Query: 179 TIYKKVVRRAGDFALVSLALAIKLRQNEIEDIRLAYGGVGERPFRALEVEKSVMGKRLND 238 ++++ R GDFA+VSLA AI Q + L GGV +RP R G L D Sbjct: 181 YRFREIAMRHGDFAIVSLAAAIGADQ-----VELGIGGVADRPQR----RSLPRGAGLPD 231 Query: 239 ELVEEIVSKVSSQVNPPSDTRGSSWYRREVMKVITRKALKEV 280 L ++ + ++ D + S+ YRR++++ + + ++ V Sbjct: 232 AL-----NQTAWSLDAQDDVQASAAYRRQLIRELGHQLIEGV 268 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: 158 Number of extensions: 6 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: 282 Length of database: 268 Length adjustment: 25 Effective length of query: 257 Effective length of database: 243 Effective search space: 62451 Effective search space used: 62451 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