Align glycolaldehyde oxidoreductase medium subunit (characterized)
to candidate H281DRAFT_02674 H281DRAFT_02674 carbon-monoxide dehydrogenase medium subunit
Query= metacyc::MONOMER-18072 (282 letters) >FitnessBrowser__Burk376:H281DRAFT_02674 Length = 293 Score = 139 bits (351), Expect = 6e-38 Identities = 88/284 (30%), Positives = 156/284 (54%), Gaps = 7/284 (2%) Query: 1 MYPPDFTYVRVSSSEEATKFLESHDDARPLAGGQSLIPMLKLRVISPNYIVDLNPITSLS 60 M P +F Y ++ +EA + L + +DAR LAGGQSL+PM+ R + ++++DLN + +L+ Sbjct: 1 MKPSEFLYHAPTTLDEAVQLLGTLEDARVLAGGQSLMPMMNFRYLMTSHLIDLNGVEALT 60 Query: 61 YVRSSFNSTKIGALTRYNEILKNDLVRVNVPLLHQAVRVVGDMQVRNLGTIGGSAANADP 120 + + IGA+ R +I + LV PL+ +A ++V Q+RN GT+GGS DP Sbjct: 61 RIEQRGDRLHIGAMARQRDIELSPLVIQRAPLIREAYQLVSHKQIRNRGTLGGSLCQLDP 120 Query: 121 SADIPTVLTALNAEIILS----SASGNRSVNALDFFKGAFATDLRKGEIISEIVLPNL-E 175 S++ P AL+ + ++ A +R + D+ L +GE+++ I L E Sbjct: 121 SSEQPCFTAALDGVLTIARYEDGAVTHRELPMSDWAVMYMTPALEEGELLAGISLDIWPE 180 Query: 176 GYRTIYKKVVRRAGDFALVSL-ALAIKLRQNEIEDIRLAYGGVGERPFRALEVEKSVMGK 234 G+ +++ RR GD+A+V + AL Q ++ + L GV P R +VE ++ G+ Sbjct: 181 GHGYAFEEFARRHGDYAIVGVAALCTADAQGNLDRVSLTICGVAPGPVRMHDVETALRGR 240 Query: 235 RLNDELVEEIVSKVSSQVNPPSDTRGSSWYRREVMKVITRKALK 278 ++D + + S +S ++ +D S+ YR+ + V+T +ALK Sbjct: 241 PMDDAAL-RMASDAASALDVMTDAHVSTDYRQHLAGVLTERALK 283 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: 147 Number of extensions: 7 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: 293 Length adjustment: 26 Effective length of query: 256 Effective length of database: 267 Effective search space: 68352 Effective search space used: 68352 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