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 PfGW456L13_3345 Oligopeptide transport system permease protein OppC (TC 3.A.1.5.1)
Query= TCDB::Q9X270 (289 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3345 Length = 339 Score = 121 bits (304), Expect = 2e-32 Identities = 76/241 (31%), Positives = 118/241 (48%), Gaps = 4/241 (1%) Query: 48 PYPYDEPHY---IRAFEGPSKDFIFGTDALGRDLFSRILYSLRNACIIGFGSQFVVLIIG 104 PY Y +Y + A PS D + GTD GRD+ +R++Y R + + + IIG Sbjct: 99 PYSYQSINYDLKVPAPAPPSTDNLLGTDDQGRDVLARVIYGFRISVLFALTLTVLSSIIG 158 Query: 105 GILGAVAGFKGGWIDKFIMSIVDIMFAFPTFLFNVILVTALGRGLFTIFLAIGLTGWAGM 164 I GA+ GF GGW+D ++I P +IL + + + + + L W + Sbjct: 159 VIAGALQGFYGGWVDLAGQRFLEIWSGLPVLYLLIILASFVQPNFWWLLGIMLLFSWMSL 218 Query: 165 ARLVRGQVLYLKNSEFVEAAKAAGASTFYIIRKHILPNMIGPILVNLAFGVPGAMMTESG 224 +VR + L +N E+V AA+A G I+ +HILPN + + + F + GA+ T + Sbjct: 219 VDVVRAEFLRGRNLEYVRAARALGMQNGAIMFRHILPNAMVSTMTFMPFILTGAIGTLTA 278 Query: 225 LAVIGMGVRPPMPSWGNLIGEGIGMMMAFPHLLIFPAVTFAFTLISFTFLADGLRDAFNP 284 L +G G+ PS G L+ +G + A P L I A L F+ + RDAF+P Sbjct: 279 LDFLGFGLPAGSPSLGELVAQGKSNLQA-PWLGISAFAVLALMLSLLVFIGESARDAFDP 337 Query: 285 R 285 R Sbjct: 338 R 338 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: 252 Number of extensions: 10 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: 289 Length of database: 339 Length adjustment: 27 Effective length of query: 262 Effective length of database: 312 Effective search space: 81744 Effective search space used: 81744 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