Align Uncharacterized protein (characterized, see rationale)
to candidate RR42_RS21295 RR42_RS21295 oxidoreductase
Query= uniprot:B2TBW0 (256 letters) >FitnessBrowser__Cup4G11:RR42_RS21295 Length = 262 Score = 122 bits (305), Expect = 1e-32 Identities = 84/253 (33%), Positives = 113/253 (44%), Gaps = 26/253 (10%) Query: 11 KVALFIPCFIDAFYPEVGIATLELLERFGIQVDYPQEQTCCGQPMANSGAHAEAAGTERV 70 +V LF C +D F P+ G+ + LLER G+ V +P+ Q+CCGQP +SG +A Sbjct: 12 QVYLFATCLVDMFVPQAGLDAVRLLEREGLTVHFPRGQSCCGQPAYSSGNPEQARAVALA 71 Query: 71 FARNFAGYDYIVGPSASCIHHVREHLTALEQTDEVKKVRA-----NAYELVEFL------ 119 FA ++ PS SC +R H L D V +A YEL EFL Sbjct: 72 QLDLFAEPWPVIVPSGSCAGMMRHHWPQLFAQDPVAGPKAALLAERVYELSEFLLHVLKV 131 Query: 120 -HDVVGAREFPWAEFPHRVGLHNSCSALRHLKEASISEVAGAPFSKPRTLLEGVKGIEFV 178 DV G P P V LH SC+A R + L++ + G+ Sbjct: 132 RFDVSGVAGQP----PETVVLHTSCAARREMGTRDHGV----------ALVDALPGVTRT 177 Query: 179 KPARPDECCGFGGTFSVTEEPVSVRMGQDKVRDHLNAGAEYIVSGDMSCLMHQQGCAERM 238 + R ECCGFGGTFS+ +S M QDK+ G + +VS D CL++ A Sbjct: 178 EHQRESECCGFGGTFSLKHPDISGAMVQDKIASACATGCDRLVSADCGCLLNIGHAARHQ 237 Query: 239 KADARFIHIAQVL 251 A HIA L Sbjct: 238 GAPLPVEHIASFL 250 Lambda K H 0.323 0.137 0.422 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: 241 Number of extensions: 14 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: 256 Length of database: 262 Length adjustment: 24 Effective length of query: 232 Effective length of database: 238 Effective search space: 55216 Effective search space used: 55216 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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