Align PTS system, IID component, component of The gluconate PTS uptake system. IIAGnt and IIBGnt form a high affinity 2:2 heterotetrameric complex (characterized)
to candidate BWI76_RS03970 BWI76_RS03970 PTS mannose/fructose/sorbose family transporter subunit IID
Query= TCDB::Q82ZC6 (290 letters) >FitnessBrowser__Koxy:BWI76_RS03970 Length = 283 Score = 126 bits (316), Expect = 6e-34 Identities = 82/268 (30%), Positives = 147/268 (54%), Gaps = 15/268 (5%) Query: 5 TEKVVPKTTNLAPEE-----ITNKDVTKAYLRWHFANEIPHSFERYLAPSLLYAMMPLLK 59 T K++ + T L P+E IT +D+ + + R F E ++ER + + +YA++P+LK Sbjct: 2 TTKMISEET-LRPQEQEETRITPRDLRRVFWR-SFQMEFSWNYERQMNLAFVYALIPVLK 59 Query: 60 KLYKDDEQLKAAYMRQLLFFNTQLSWGGGVITGLMASMEQERAKEEHEGREIMMQDDLMY 119 KLY E+L AA R L+FFNT ++ G+ +ME++ +++++ M + + Sbjct: 60 KLYPRKEELAAALKRHLVFFNTTPHIVT-LLLGITTAMEEKNSQQKN------MDANAID 112 Query: 120 NTKAGLMGALAGIGDAIDSGTVQYIFIAIAVPWAQQGSALGAIFPFVAFALYQVLLGVFF 179 N KA LMG LAG+GD+ GT++ I I A +G+ LG I + F + +L+ FF Sbjct: 113 NVKASLMGPLAGLGDSFFWGTLRLIATGIGTSLALKGNILGPILFLLVFNVPHILVRWFF 172 Query: 180 ARQSFKMGRNATGLMQSAGIQKAIEM-LSVLGLFMMGILAGNYVKVSSTLQFKLSGREFV 238 R + +G +Q +G+ +++ S++GL ++G + + + ++ + F + Sbjct: 173 TRWGYVLGTGVLQRIQKSGMMESLTYGASIIGLMVVGAMTASMIDITIPVSFGAGEAKTQ 232 Query: 239 VQDILDQIVPGLLPLAVVMGVYWFYTKK 266 VQDI++ I+P +LPL VYW +K Sbjct: 233 VQDIINDILPCMLPLLSFGIVYWLLGRK 260 Lambda K H 0.324 0.138 0.402 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: 234 Number of extensions: 13 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: 290 Length of database: 283 Length adjustment: 26 Effective length of query: 264 Effective length of database: 257 Effective search space: 67848 Effective search space used: 67848 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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