Align major cell-binding factor (characterized)
to candidate BWI76_RS05960 BWI76_RS05960 cysteine transport system periplasmic binding protein
Query= CharProtDB::CH_021449 (259 letters) >FitnessBrowser__Koxy:BWI76_RS05960 Length = 269 Score = 104 bits (259), Expect = 2e-27 Identities = 80/241 (33%), Positives = 120/241 (49%), Gaps = 16/241 (6%) Query: 14 ALGACVAFSNANAAEGKLESIKSKGQLIVGVKNDVPHYALLDQATGEIKGFEVDVAKLLA 73 ALG V + A A + L IK+ G + V + P + +D T +I G++VD A+ LA Sbjct: 11 ALGMLVLAAQAQADQ--LADIKAAGVVKVATFDANPPFGSVDPKTHKIVGYDVDFAEALA 68 Query: 74 KSILGDDKKIKLVAVNAKTRGPLLDNGSVDAVIATFTITPERKRIYNFSEPYYQDAIGLL 133 KS+ K++LVA N R PLL +G D ++A TITPER ++ +FS PY+ L Sbjct: 69 KSL---GVKLELVATNPANRIPLLQSGKADLIVADITITPERAQVIDFSTPYFVTGQQFL 125 Query: 134 VLKEKKYKSLADMKGANIGVAQAATTKKAIGEAAKKIGIDVKFSEFPDYPSIKAALDAKR 193 V K L D A IG + T ++A+ + + + + D P AL Sbjct: 126 V-PAKSPDKLDDYSKARIGAVKGTTGEQALHQRFPQ----SRVLSYDDIPLALTALRNGN 180 Query: 194 VDAFSVDKSILLGYV---DDKS--EILPDSFEPQSYGIVTKKDDPAFAKYV-DDFVKEHK 247 V A + D +IL G + DK+ +I+PD + G+ KK +P K V D+ VK K Sbjct: 181 VQAITQDSTILAGLLAEAPDKANFKIIPDLLSKEEIGVGVKKGEPTLLKAVNDELVKLEK 240 Query: 248 N 248 + Sbjct: 241 S 241 Lambda K H 0.316 0.135 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: 161 Number of extensions: 11 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: 259 Length of database: 269 Length adjustment: 25 Effective length of query: 234 Effective length of database: 244 Effective search space: 57096 Effective search space used: 57096 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 (21.6 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