Align LUD_dom domain-containing protein (characterized, see rationale)
to candidate AO356_07560 AO356_07560 (Fe-S)-binding protein
Query= uniprot:Q726S4 (209 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_07560 Length = 489 Score = 52.0 bits (123), Expect = 2e-11 Identities = 34/115 (29%), Positives = 56/115 (48%), Gaps = 12/115 (10%) Query: 98 REGLRKHLAGIDIGFTHVTMGIAETGTCVVSSNSEELRLASMISEFHVAVLPKSKIVATS 157 R+ LR+ DIG + V +AETGT ++ N R+++ + H+AV K+V Sbjct: 199 RKVLRQKFFEADIGVSGVNFAVAETGTLLLVENEGNGRMSTTVPPVHIAVTGIEKVVENL 258 Query: 158 YDAEATLNEL----MGTGKPHYTAFISGPSRTADIERVLSLGVHGPLELHLILVE 208 D L+ L +G Y ISGP + +++ GP E+HL+L++ Sbjct: 259 RDVVPLLSLLTRSALGQPITTYVNMISGPRKADELD--------GPQEVHLVLLD 305 Lambda K H 0.317 0.132 0.371 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: 193 Number of extensions: 9 Number of successful extensions: 1 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: 209 Length of database: 489 Length adjustment: 27 Effective length of query: 182 Effective length of database: 462 Effective search space: 84084 Effective search space used: 84084 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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