Align 2-deoxy-D-ribose dehydrogenase α subunit (characterized)
to candidate WP_012759947.1 RLEG_RS32870 (2Fe-2S)-binding protein
Query= metacyc::MONOMER-20832 (151 letters) >NCBI__GCF_000023185.1:WP_012759947.1 Length = 174 Score = 132 bits (332), Expect = 3e-36 Identities = 63/143 (44%), Positives = 90/143 (62%), Gaps = 1/143 (0%) Query: 1 MELRINQKAYQVDADADTPLLWVIRDDLGLTGTKYGCGLAQCGACSVLVDGNVVRSCVTP 60 + L +N ++V A +TPLL+++R+DL L G KYGCGL +CGAC+VLVDG VRSC P Sbjct: 7 VSLNVNDALWRVSAKPETPLLYILRNDLCLNGPKYGCGLGECGACAVLVDGRPVRSCTVP 66 Query: 61 VAGVVGREITTIEAIETDEVGKRVVATWVEHQVAQCGYCQSGQVMAATALLKHTPAPSKA 120 + + R + T+E + D + V ++E AQCGYC +G ++A LL+ P ++ Sbjct: 67 LGAIGKRRVITLEGLAVDGLLHPVQQAFIEEAAAQCGYCLNGMIIATVGLLQRNTDPDES 126 Query: 121 QI-DAAMINLCRCGTYNAIHAAV 142 I DA +LCRCGT+ I AAV Sbjct: 127 DIRDALRHHLCRCGTHVEILAAV 149 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: 104 Number of extensions: 4 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: 174 Length adjustment: 18 Effective length of query: 133 Effective length of database: 156 Effective search space: 20748 Effective search space used: 20748 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 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