Align PTS system IID component, Man family, component of The hexose (glucose and fructose demonstrated) PTS uptake system (characterized)
to candidate WP_045477156.1 TT13_RS09605 PTS mannose/fructose/sorbose transporter family subunit IID
Query= TCDB::Q04GJ9 (304 letters) >NCBI__GCF_000691805.2:WP_045477156.1 Length = 324 Score = 380 bits (977), Expect = e-110 Identities = 188/317 (59%), Positives = 244/317 (76%), Gaps = 17/317 (5%) Query: 5 KITLTKGDRLHVAWRSTFIQGSWNYERMQNGGWVYALIPALNKLYKT-KEDRAAAYKRHL 63 K+TL+KG R V S FIQGSWNYERMQN GW ++L+PAL +LYK E+ A +RH+ Sbjct: 8 KVTLSKGTRFKVMMSSMFIQGSWNYERMQNVGWAFSLMPALKRLYKPGTEEAKLALQRHM 67 Query: 64 VFFNTHPYLASPIIGVTLALEEDRANGAPVDDVAIQGVKVGMMGPLAGVGDPVFWYTVRP 123 FFNTHPYLASPI+GVTLALEE+RANGA +D+ AIQGVKVGMMGPLAG+GDPVFW+TVRP Sbjct: 68 EFFNTHPYLASPILGVTLALEEERANGAKIDNAAIQGVKVGMMGPLAGIGDPVFWFTVRP 127 Query: 124 LLGALGATLALSGNVLGPILFWVLWNIIRWAFMWYTQEFGYRAGSRITDDLSGGLLKTVT 183 ++GA+ A+LA+SG+++ PI+F+V WNIIR AF+WYTQEFGY+ G+ IT DL GG+L+ VT Sbjct: 128 IIGAIAASLAVSGSIIAPIVFFVAWNIIRIAFLWYTQEFGYKQGTAITGDLGGGMLQKVT 187 Query: 184 RGASMMGMFVLAALIERWVSIKFT---PVVSKVTLSKGAYIDWGKLPSGTKGIREALTE- 239 +GAS++GMFVL ALI+RWVSI +T VVSK+ LSKGAY+DW LPSG +GI+ A+T Sbjct: 188 KGASILGMFVLGALIQRWVSISWTGPNSVVSKLPLSKGAYLDWNSLPSGAQGIKTAITTL 247 Query: 240 ---------QANGLSLTKIQTTTLQQNLDSLIPGLMALLLTFACMWLLKK---KVSPIII 287 +G+ +T + T LQ NL+ L+PGL ALLLTF +WLL+K + +P+ I Sbjct: 248 FKQDASGNLTQSGVYMTPNKITYLQDNLNMLLPGLSALLLTFLVIWLLRKFKSRNTPLYI 307 Query: 288 ILGIFVIGVGGHLLGLL 304 I+G+F+ G+ H GL+ Sbjct: 308 IIGLFIFGILLHWAGLM 324 Lambda K H 0.324 0.140 0.438 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: 393 Number of extensions: 14 Number of successful extensions: 4 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: 304 Length of database: 324 Length adjustment: 27 Effective length of query: 277 Effective length of database: 297 Effective search space: 82269 Effective search space used: 82269 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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