Align major cell-binding factor (characterized)
to candidate WP_054653754.1 CES79_RS00810 transporter substrate-binding domain-containing protein
Query= CharProtDB::CH_021449 (259 letters) >NCBI__GCF_002217945.1:WP_054653754.1 Length = 277 Score = 114 bits (285), Expect = 2e-30 Identities = 74/229 (32%), Positives = 112/229 (48%), Gaps = 10/229 (4%) Query: 35 KSKGQLIVGVKNDVPHYALLDQATGEIKGFEVDVAKLLAKSILGDDKKIKLVAVNAKTRG 94 K + GVK D + L+D +IKGFEVD+AK L K ILG K V V + TR Sbjct: 39 KQSNTITWGVKADTKLFGLMDVKNSQIKGFEVDMAKALTKQILGPKGKADFVQVTSSTRM 98 Query: 95 PLLDNGSVDAVIATFTITPERKRIYNFSEPYYQDAIGLLVLKEKKYKSLADM--KGANIG 152 PLL NG++DA++AT TITPER + +FS Y+ LLV K++ D+ GA + Sbjct: 99 PLLKNGNIDAIMATMTITPERLKQVDFSRSYFDAGQSLLVKNGSPIKNVKDLNKNGATVL 158 Query: 153 VAQAATTKKAIGEAAKKIGIDVKFSEFPDYPSIKAALDAKRVDAFSVDKSILLGYVDDKS 212 + + + + + A K K + DY AL + + +A + D IL G + Sbjct: 159 GVVGSNSVQNVAKFAPK----AKVLQLSDYAQAMTALKSGQGEALTTDNGILAGMSVENP 214 Query: 213 --EILPDSFEPQSYGIVTKKDDPAFAKYVDDFVK--EHKNEIDALAKKW 257 + +F + YGI K+ P F ++ + E + + + KKW Sbjct: 215 GYHLAGGAFTKEPYGIAINKNQPEFKHDLNHALTKVEQSGQYNRILKKW 263 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: 12 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: 259 Length of database: 277 Length adjustment: 25 Effective length of query: 234 Effective length of database: 252 Effective search space: 58968 Effective search space used: 58968 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