Align 2-deoxy-D-ribose dehydrogenase α subunit (characterized)
to candidate AZOBR_RS30035 AZOBR_RS30035 (2Fe-2S)-binding protein
Query= metacyc::MONOMER-20832 (151 letters) >FitnessBrowser__azobra:AZOBR_RS30035 Length = 152 Score = 157 bits (398), Expect = 5e-44 Identities = 79/151 (52%), Positives = 99/151 (65%), Gaps = 2/151 (1%) Query: 1 MELRINQKAYQVDADADTPLLWVIRDDLGLTGTKYGCGLAQCGACSVLVDGNVVRSCVTP 60 + L IN + VD D PLLWV+RD+L LTGTK+GCG+AQCGAC+V +DG +R+C TP Sbjct: 2 IRLNINGQDRDVDVPGDMPLLWVLRDELNLTGTKFGCGIAQCGACTVHMDGTPIRACQTP 61 Query: 61 VAGVVGREITTIEAIETDEVGKRVVATWVEHQVAQCGYCQSGQVMAATALLKHTPAPSKA 120 G +ITTIE + + V + V A W + V QCGYCQSGQ+M+A ALL P+ Sbjct: 62 AESAAGTKITTIEGV-SGTVAQAVQAAWQKLDVVQCGYCQSGQIMSAVALLTDNRNPTDD 120 Query: 121 QIDAAMI-NLCRCGTYNAIHAAVDDLAKQGG 150 IDAAM N+CRC TY I AA+ D AK G Sbjct: 121 DIDAAMDGNVCRCATYPRIRAAIKDAAKAMG 151 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: 127 Number of extensions: 9 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: 152 Length adjustment: 17 Effective length of query: 134 Effective length of database: 135 Effective search space: 18090 Effective search space used: 18090 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