Align 2-deoxy-D-ribose dehydrogenase α subunit (characterized)
to candidate AO353_00730 AO353_00730 FAD-binding molybdopterin dehydrogenase
Query= metacyc::MONOMER-20832 (151 letters) >FitnessBrowser__pseudo3_N2E3:AO353_00730 Length = 484 Score = 73.9 bits (180), Expect = 3e-18 Identities = 55/165 (33%), Positives = 84/165 (50%), Gaps = 17/165 (10%) Query: 1 MELRINQKAYQVDA-DADTPLLWVIRDDLGLTGTKYGCGLAQCGACSVLV-----DGN-- 52 ++ +NQ+ A D + +L +R+ LG GTK GC CGAC+V+V D N Sbjct: 2 IQFLLNQELRSEHALDPNLTVLNYLREHLGKPGTKEGCASGDCGACTVVVGELQTDDNGR 61 Query: 53 ------VVRSCVTPVAGVVGREITTIEAIETDEVGKRVVATWVEHQVAQCGYCQSGQVMA 106 + SC+T V+ + G+++ ++E ++ V VE +QCG+C G VM+ Sbjct: 62 EHIRYRSLNSCLTFVSSLHGKQLISVEDLKHQGKLHSVQKAMVECHGSQCGFCTPGFVMS 121 Query: 107 ATALLKHTP-APSKAQIDAAMINLCRCGTYNAIHAAVDDL--AKQ 148 AL K++ A S +A NLCRC Y I AA + + AKQ Sbjct: 122 LFALQKNSDHADSHKAHEALAGNLCRCTGYRPILAAAEQVCSAKQ 166 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: 161 Number of extensions: 10 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: 484 Length adjustment: 25 Effective length of query: 126 Effective length of database: 459 Effective search space: 57834 Effective search space used: 57834 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: 47 (22.7 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