Align 2-deoxy-D-ribose dehydrogenase α subunit (characterized)
to candidate CCNA_02353 CCNA_02353 membrane-bound aldehyde dehydrogenase iron-sulfur protein
Query= metacyc::MONOMER-20832 (151 letters) >FitnessBrowser__Caulo:CCNA_02353 Length = 154 Score = 163 bits (413), Expect = 1e-45 Identities = 79/141 (56%), Positives = 99/141 (70%), Gaps = 1/141 (0%) Query: 3 LRINQKAYQVDADADTPLLWVIRDDLGLTGTKYGCGLAQCGACSVLVDGNVVRSCVTPVA 62 L +N ++ D D DTPLLWV+RD LGL GTKYGCG A CGAC+V +DG VR+CVTP++ Sbjct: 5 LTVNGESRIADVDGDTPLLWVLRDTLGLVGTKYGCGAALCGACTVHLDGVPVRACVTPIS 64 Query: 63 GVVGREITTIEAIETDEVGKRVVATWVEHQVAQCGYCQSGQVMAATALLKHTPAPSKAQI 122 GV +++TTIE + VG +V A W QCGYCQ+GQ+M+ATALL TP P+ +I Sbjct: 65 GVGEQKVTTIEGVGKTTVGAKVQAAWKAVDTPQCGYCQAGQIMSATALLATTPKPTDEEI 124 Query: 123 DAAMI-NLCRCGTYNAIHAAV 142 DAAM NLCRC TY I A+ Sbjct: 125 DAAMNGNLCRCATYIRIKKAI 145 Lambda K H 0.320 0.134 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: 129 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: 151 Length of database: 154 Length adjustment: 17 Effective length of query: 134 Effective length of database: 137 Effective search space: 18358 Effective search space used: 18358 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: 43 (21.2 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