Align major cell-binding factor (characterized)
to candidate YP_004143089.1 Mesci_3923 family 3 extracellular solute-binding protein
Query= CharProtDB::CH_021449 (259 letters) >NCBI__GCF_000185905.1:YP_004143089.1 Length = 261 Score = 75.9 bits (185), Expect = 8e-19 Identities = 63/206 (30%), Positives = 92/206 (44%), Gaps = 23/206 (11%) Query: 8 LKLAVFALGACVAFSNANAAEGKLESIKSKGQLIVGVKNDVPHYALLDQATGEIKGFEVD 67 L++A+ A A + A A E L +G + P + L A G++ GF++D Sbjct: 5 LRIALAASAALLTLGVAQAQEKTLR---------IGTEGAYPPFNNLT-ADGQLVGFDID 54 Query: 68 VAKLLAKSILGDDKKIKLVAVNAKTRG--PLLDNGSVDAVIATFTITPERKRIYNFSEPY 125 +AK L D+ K+K V G P L G DA++A+ +ITPERK +FS Y Sbjct: 55 IAKALC-----DEMKVKCTFVAQDWDGIIPALQAGKFDAIVASMSITPERKEKVDFSNKY 109 Query: 126 YQDAIGLLVLKEKKYKSLA--DMKGANIGVAQAATTKKAIGEAAKKIGIDVKFSEFPDYP 183 Y + V K+ K + D+ G IGVA T A K D +P P Sbjct: 110 YNTPSAIAVPKDSTLKGVTKEDLAGKTIGVATTTTH----FNYASKTYTDSTVKGYPSSP 165 Query: 184 SIKAALDAKRVDAFSVDKSILLGYVD 209 +A L R+DA D +L ++D Sbjct: 166 EEQADLANGRLDAIEDDIVVLQQFLD 191 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: 154 Number of extensions: 11 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: 259 Length of database: 261 Length adjustment: 24 Effective length of query: 235 Effective length of database: 237 Effective search space: 55695 Effective search space used: 55695 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 24 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