Align TM1748, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate BPHYT_RS22040 BPHYT_RS22040 peptide ABC transporter permease
Query= TCDB::Q9X270 (289 letters) >FitnessBrowser__BFirm:BPHYT_RS22040 Length = 304 Score = 196 bits (498), Expect = 5e-55 Identities = 106/273 (38%), Positives = 161/273 (58%), Gaps = 3/273 (1%) Query: 15 AFWLRFKKNKMAVIGGVFVLILIALAILAPYIAPYPYDEPHYIRAFEGPSKDFI--FGTD 72 A W RF +N+ A G V +++++ + P++ P + + P+ + FGTD Sbjct: 31 AAW-RFVRNRAAFAGFVVLMLIVIACVAGPWLLPNNPIDSDWSAISLPPTLQNMHWFGTD 89 Query: 73 ALGRDLFSRILYSLRNACIIGFGSQFVVLIIGGILGAVAGFKGGWIDKFIMSIVDIMFAF 132 LGRDL +R L R + +G V +IG GA AG+ GG +D +M IVD+M+A Sbjct: 90 ELGRDLLARTLQGGRVSLEVGLLGTLVSGLIGVAYGATAGYLGGRVDAVMMRIVDMMYAI 149 Query: 133 PTFLFNVILVTALGRGLFTIFLAIGLTGWAGMARLVRGQVLYLKNSEFVEAAKAAGASTF 192 P L ++++T GR + + L I W MAR+VRGQ L L++ EF++AA+A G S+ Sbjct: 150 PYMLIAILMMTMFGRAFYLVVLTISAFSWLDMARVVRGQTLSLRSREFIDAARAIGVSSG 209 Query: 193 YIIRKHILPNMIGPILVNLAFGVPGAMMTESGLAVIGMGVRPPMPSWGNLIGEGIGMMMA 252 II +HI+PN+ G ++V + VP ++TES L+ +G+GV+ PM SWG LI +G + + Sbjct: 210 SIIARHIVPNLFGVVVVYASVTVPNIVLTESVLSFLGLGVQEPMTSWGVLIQDGAQKLES 269 Query: 253 FPHLLIFPAVTFAFTLISFTFLADGLRDAFNPR 285 P LL+ PAV TL F+ DGLRDAF+P+ Sbjct: 270 MPWLLLCPAVMLCVTLYCVNFVGDGLRDAFDPK 302 Lambda K H 0.331 0.147 0.457 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: 214 Number of extensions: 6 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: 289 Length of database: 304 Length adjustment: 26 Effective length of query: 263 Effective length of database: 278 Effective search space: 73114 Effective search space used: 73114 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 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