Align 2-deoxy-D-ribose dehydrogenase α subunit (characterized)
to candidate WP_011937928.1 GURA_RS05055 molybdopterin cofactor-binding domain-containing protein
Query= metacyc::MONOMER-20832 (151 letters) >NCBI__GCF_000016745.1:WP_011937928.1 Length = 931 Score = 96.7 bits (239), Expect = 9e-25 Identities = 56/137 (40%), Positives = 75/137 (54%), Gaps = 4/137 (2%) Query: 15 DADTPLLWVIRDDLGLTGTKYGCGLAQCGACSVLVDGNVVRSCVTPVAGVVG-REITTIE 73 D + L V+R L LTGTK GCG QCGAC+V++DG +VRSCV + V +ITTIE Sbjct: 18 DQEALLSDVLRKQLHLTGTKVGCGTGQCGACNVIMDGKLVRSCVVKMKKVENLAKITTIE 77 Query: 74 AIETDEVGKRVVATWVEHQVAQCGYCQSGQVMAATALLKHTPAPSKAQID---AAMINLC 130 I T + ++ H QCG+C G +++ ALL P P++ + N C Sbjct: 78 GIGTPLNLHPIQKAFIFHGALQCGFCTPGFIVSTKALLDENPNPTREDVRDWFQKYRNAC 137 Query: 131 RCGTYNAIHAAVDDLAK 147 RC Y+ I AV D AK Sbjct: 138 RCTGYSMIVDAVMDAAK 154 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: 357 Number of extensions: 27 Number of successful extensions: 3 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: 931 Length adjustment: 29 Effective length of query: 122 Effective length of database: 902 Effective search space: 110044 Effective search space used: 110044 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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