Align 2-deoxy-D-ribose dehydrogenase α subunit (characterized)
to candidate WP_043743639.1 AMB_RS06625 (2Fe-2S)-binding protein
Query= metacyc::MONOMER-20832 (151 letters) >NCBI__GCF_000009985.1:WP_043743639.1 Length = 169 Score = 124 bits (311), Expect = 7e-34 Identities = 60/130 (46%), Positives = 82/130 (63%), Gaps = 1/130 (0%) Query: 14 ADADTPLLWVIRDDLGLTGTKYGCGLAQCGACSVLVDGNVVRSCVTPVAGVVGREITTIE 73 AD D PL++ +R++LGLTGT GCG +CGAC+VL+DG RSC T + G+ +TTIE Sbjct: 31 ADGDMPLVYWLREELGLTGTHLGCGKGECGACTVLIDGQPARSCRTTLGEAAGKVVTTIE 90 Query: 74 AIETDEVGKRVVATWVEHQVAQCGYCQSGQVMAATALLKHTPAPSKAQIDAAMI-NLCRC 132 + T E V A +VE Q AQCG+C G V+ ALL T P A++ A+ +LCRC Sbjct: 91 GLGTPEAPHPVQAAFVEEQAAQCGFCTPGMVVEGAALLARTAQPDLAEVKEALDGHLCRC 150 Query: 133 GTYNAIHAAV 142 G++ + AV Sbjct: 151 GSHQRVLKAV 160 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: 105 Number of extensions: 7 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: 169 Length adjustment: 17 Effective length of query: 134 Effective length of database: 152 Effective search space: 20368 Effective search space used: 20368 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