Align Sulfur carrier protein CysO; 9.5 kDa culture filtrate antigen cfp10A (characterized)
to candidate Synpcc7942_1781 Synpcc7942_1781 hypothetical protein
Query= SwissProt::P9WP33 (93 letters) >FitnessBrowser__SynE:Synpcc7942_1781 Length = 91 Score = 82.8 bits (203), Expect = 8e-22 Identities = 41/93 (44%), Positives = 60/93 (64%), Gaps = 2/93 (2%) Query: 1 MNVTVSIPTILRPHTGGQKSVSASGDTLGAVISDLEANYSGISERLMDPSSPGKLHRFVN 60 M +TV IPT L+ T Q S+ + +++ LE ++ GI RL D G+L RF+N Sbjct: 1 MAITVLIPTPLQKFTNNQASLECEASDVKSLLEALEQSFPGIKARLCDEQ--GQLRRFLN 58 Query: 61 IYVNDEDVRFSGGLATAIADGDSVTILPAVAGG 93 +YVN ED+RF G+ T++ +GD V+I+PAVAGG Sbjct: 59 VYVNSEDIRFLDGIQTSLGNGDEVSIVPAVAGG 91 Lambda K H 0.313 0.133 0.372 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: 46 Number of extensions: 3 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: 93 Length of database: 91 Length adjustment: 9 Effective length of query: 84 Effective length of database: 82 Effective search space: 6888 Effective search space used: 6888 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 39 (20.5 bits) S2: 39 (19.6 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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