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 Ac3H11_696 Dipeptide transport system permease protein DppC (TC 3.A.1.5.2)
Query= TCDB::Q9X270 (289 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_696 Length = 287 Score = 155 bits (393), Expect = 8e-43 Identities = 87/278 (31%), Positives = 149/278 (53%), Gaps = 8/278 (2%) Query: 15 AFWLRFKK-------NKMAVIGGVFVLILIALAILAPYIAPYPYDEPHYIRAFEGPSKDF 67 +FW R + K+ + + + ++ ++A++ P+++ + PS Sbjct: 6 SFWHRLRAVLRRLFARKVVLASAIVITLVASIAVVFPWVSDADPNALSISERLHAPSGTH 65 Query: 68 IFGTDALGRDLFSRILYSLRNACIIGFGSQFVVLIIGGILGAVAGFKGGWIDKFIMSIVD 127 GTD LGRD+ RI++ R + +IG + +++G +LG +AGF +D +M +VD Sbjct: 66 WAGTDELGRDVLLRIVHGARYSLLIGLVTAAGAVLLGTLLGMLAGFFRR-LDAPLMRLVD 124 Query: 128 IMFAFPTFLFNVILVTALGRGLFTIFLAIGLTGWAGMARLVRGQVLYLKNSEFVEAAKAA 187 M +FP L + LV+ LG L+ + LA+ + +AR+VR L L+ FV+AA+A Sbjct: 125 AMMSFPDILLGIALVSILGVSLWNVMLALVIVYTPRVARVVRATTLVLRELLFVDAARAL 184 Query: 188 GASTFYIIRKHILPNMIGPILVNLAFGVPGAMMTESGLAVIGMGVRPPMPSWGNLIGEGI 247 G T I+ +HILPN++ PILV + F A++ E+GL+ +G+GV P +P+WG +I + Sbjct: 185 GVRTHLILWRHILPNLMSPILVQVTFIFAYAILAEAGLSFLGVGVPPDIPTWGTMIAGSL 244 Query: 248 GMMMAFPHLLIFPAVTFAFTLISFTFLADGLRDAFNPR 285 + P V T +S L DG+RD +P+ Sbjct: 245 DYADKAFWTIFAPGVAIVLTALSLQMLGDGVRDLLDPK 282 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: 212 Number of extensions: 10 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: 287 Length adjustment: 26 Effective length of query: 263 Effective length of database: 261 Effective search space: 68643 Effective search space used: 68643 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: 47 (22.7 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