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 Synpcc7942_0445 Synpcc7942_0445 ABC-type dipeptide/oligopeptide/nickel transport systems permease components-like
Query= TCDB::Q9X270 (289 letters) >FitnessBrowser__SynE:Synpcc7942_0445 Length = 351 Score = 169 bits (428), Expect = 8e-47 Identities = 85/232 (36%), Positives = 137/232 (59%), Gaps = 8/232 (3%) Query: 62 GPSKDFIFGTDALGRDLFSRILYSLRNACIIGFGSQFVVLIIGGILGAVAGFKGGWIDKF 121 GP K + GTD GRD FSR+LY R + +G + +G ++G +AG+ GGW+D Sbjct: 119 GPGKLHLLGTDDQGRDQFSRLLYGSRISLSVGLVGVILTFPLGILVGGIAGYWGGWVDAL 178 Query: 122 IMSIVDIMFAFPTFLFNVILVTALGRGL-----FTIFLAI-GLTGWAGMARLVRGQVLYL 175 IM +V+++ P+ V L L GL F + +AI L WAG+AR++RGQVL L Sbjct: 179 IMRLVEVLMTIPSLYLLVALAAVLPPGLSSAERFLLIVAITSLINWAGLARVIRGQVLSL 238 Query: 176 KNSEFVEAAKAAGASTFYIIRKHILPNMIGPILVNLAFGVPGAMMTESGLAVIGMGVRPP 235 + E+V+A++ GAS Y++ +HILP + +++ VP ++ ES L+++G+G++ P Sbjct: 239 REREYVQASQVMGASRLYLLIRHILPQTLTYVIIAATLAVPSFIVAESVLSLVGLGIQQP 298 Query: 236 MPSWGNL--IGEGIGMMMAFPHLLIFPAVTFAFTLISFTFLADGLRDAFNPR 285 PSWGN+ + M++ P L+ PA+ +++F + DGLRD +PR Sbjct: 299 DPSWGNMLSLATNASMLLLNPWLIWPPALLIVVAVLAFNVVGDGLRDRLDPR 350 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: 261 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: 289 Length of database: 351 Length adjustment: 27 Effective length of query: 262 Effective length of database: 324 Effective search space: 84888 Effective search space used: 84888 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