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 Pf6N2E2_3231 Dipeptide transport system permease protein DppC (TC 3.A.1.5.2)
Query= TCDB::Q9X270 (289 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3231 Length = 300 Score = 179 bits (453), Expect = 9e-50 Identities = 96/271 (35%), Positives = 149/271 (54%), Gaps = 1/271 (0%) Query: 18 LRFK-KNKMAVIGGVFVLILIALAILAPYIAPYPYDEPHYIRAFEGPSKDFIFGTDALGR 76 LRF +N M G + V L+ +A+ AP+IA + + A + PS FGTD GR Sbjct: 29 LRFLLRNPMTFAGLIVVATLMLVAVFAPWIAGHDPLLQNLAGALQAPSGVHWFGTDEYGR 88 Query: 77 DLFSRILYSLRNACIIGFGSQFVVLIIGGILGAVAGFKGGWIDKFIMSIVDIMFAFPTFL 136 D+F+R++Y R I +V IG ++G V+G+ GGW+D M I DI +FP+ + Sbjct: 89 DVFARLVYGSRITLYIVLLVTVIVGPIGLLVGTVSGYFGGWVDSLFMRITDIFISFPSLV 148 Query: 137 FNVILVTALGRGLFTIFLAIGLTGWAGMARLVRGQVLYLKNSEFVEAAKAAGASTFYIIR 196 + + ALG GL +AI LT W +ARL R + L L+N++FV A + GAS+ II Sbjct: 149 LALAFIAALGPGLEHAVIAIALTAWPPIARLARAETLPLRNADFVVAVQLQGASSTRIIL 208 Query: 197 KHILPNMIGPILVNLAFGVPGAMMTESGLAVIGMGVRPPMPSWGNLIGEGIGMMMAFPHL 256 +HI+P + +++ L + ++T + L +G+G + P+P WG +I G M+ L Sbjct: 209 RHIIPMCLSSVIIRLTMNMASIILTAAALGFLGLGAQAPLPEWGAMISTGRRYMLESWWL 268 Query: 257 LIFPAVTFAFTLISFTFLADGLRDAFNPRSE 287 + P ++F L DGLRD +PRS+ Sbjct: 269 VAAPGAAIMLVSLAFNLLGDGLRDVLDPRSQ 299 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: 199 Number of extensions: 9 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: 300 Length adjustment: 26 Effective length of query: 263 Effective length of database: 274 Effective search space: 72062 Effective search space used: 72062 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