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_5056 Dipeptide transport system permease protein DppC (TC 3.A.1.5.2)
Query= TCDB::Q9X270 (289 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5056 Length = 305 Score = 172 bits (437), Expect = 6e-48 Identities = 98/281 (34%), Positives = 150/281 (53%), Gaps = 10/281 (3%) Query: 13 WKAFWLRFKKNKMAVIGGVFVLILIALAILAPYIAPYPYDEPHYIRAF--------EGPS 64 +K FW F KNK AV G +F+L++I AI AP++AP+ E + R F EG Sbjct: 22 YKEFWQAFSKNKGAVAGLMFMLLVIFCAIFAPWVAPHDPSEQY--RDFLLTPPAWLEGGQ 79 Query: 65 KDFIFGTDALGRDLFSRILYSLRNACIIGFGSQFVVLIIGGILGAVAGFKGGWIDKFIMS 124 F+ GTD LGRDL SR++ R + +IG S + LI G +LG AGF + IM Sbjct: 80 MQFLLGTDELGRDLLSRLIQGSRLSLLIGLSSVVMSLIPGILLGLFAGFFPRILGPSIMR 139 Query: 125 IVDIMFAFPTFLFNVILVTALGRGLFTIFLAIGLTGWAGMARLVRGQVLYLKNSEFVEAA 184 ++DIM A P+ L V +V LG GL +AI + RL R V+ N ++V AA Sbjct: 140 LMDIMLALPSLLLAVAIVAILGPGLINTVIAIAVVSLPSYVRLTRAAVMGELNRDYVTAA 199 Query: 185 KAAGASTFYIIRKHILPNMIGPILVNLAFGVPGAMMTESGLAVIGMGVRPPMPSWGNLIG 244 + AGA ++ +LPN + P++V A++ + L +G+GV+PP P WG ++ Sbjct: 200 RLAGAGLPRLMFVTVLPNCMAPLIVQATLSFSSAILDAAALGFLGLGVQPPTPEWGTMLA 259 Query: 245 EGIGMMMAFPHLLIFPAVTFAFTLISFTFLADGLRDAFNPR 285 + ++ P +T ++++ + DGLRDA +P+ Sbjct: 260 SARDYIERAWWVVSLPGLTILLSVLAINLMGDGLRDALDPK 300 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: 229 Number of extensions: 12 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: 305 Length adjustment: 26 Effective length of query: 263 Effective length of database: 279 Effective search space: 73377 Effective search space used: 73377 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