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 3607469 Dshi_0882 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= TCDB::Q9X270 (289 letters) >FitnessBrowser__Dino:3607469 Length = 322 Score = 182 bits (463), Expect = 7e-51 Identities = 104/299 (34%), Positives = 160/299 (53%), Gaps = 23/299 (7%) Query: 9 SIGYWKAFWLRFKKNKMAVIGGVFVLILIALAILAPYIAPYPYDEPHYIRAFEGPSKD-- 66 S+ + F +F+++ +A++ V++L+ A+ AP IAPY P + G S Sbjct: 23 SVAWQSDFAWKFRRSPVALVSFSVVVLLVLAALFAPLIAPYDPFNPASLNLMNGFSAPMT 82 Query: 67 --------FIFGTDALGRDLFSRILYSLRNACIIGFGSQFVVLIIGGILGAVAGFKGGWI 118 F GTD GRD+FS ILY +R + +GF + + +G LG +AG+ GGW+ Sbjct: 83 PNAFTGDTFWLGTDDQGRDVFSTILYGMRISLFVGFAAVLFAMTLGVTLGLIAGYVGGWV 142 Query: 119 DKFIMSIVDIMFAFPTFLFNVILVTALGRGL-----------FTIFLAIGLTGWAGMARL 167 + IM + D+ FP L +L+ + +G+ + + LAIGL+ W AR+ Sbjct: 143 ETIIMRVADVQLTFPAILV-AMLIFGIAKGITPVEYRDQMAIWVLILAIGLSDWVQFARV 201 Query: 168 VRGQVLYLKNSEFVEAAKAAGASTFYIIRKHILPNMIGPILVNLAFGVPGAMMTESGLAV 227 VRG L KN E+V+AA+ G + I+ +HILPN++ P+LV + A++ E+ L+ Sbjct: 202 VRGATLVEKNKEYVQAARLIGRGSGAIMLRHILPNVLSPVLVIATISLALAIIAEATLSF 261 Query: 228 IGMGVRPPMPSWGNLIGEGIGMMMAFP-HLLIFPAVTFAFTLISFTFLADGLRDAFNPR 285 +G+G P PS G LI G G + + +L FPAVT +S L D LRDA NPR Sbjct: 262 LGVGAPPTQPSLGTLIRIGQGFLFSGEWWILFFPAVTLLVLALSVNLLGDWLRDALNPR 320 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: 265 Number of extensions: 9 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: 322 Length adjustment: 27 Effective length of query: 262 Effective length of database: 295 Effective search space: 77290 Effective search space used: 77290 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