Align MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate Dsui_2943 Dsui_2943 ABC-type spermidine/putrescine transport system, ATPase component
Query= TCDB::P96483 (377 letters) >FitnessBrowser__PS:Dsui_2943 Length = 356 Score = 189 bits (481), Expect = 8e-53 Identities = 99/221 (44%), Positives = 138/221 (62%), Gaps = 7/221 (3%) Query: 21 VDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTH----LPPKD 76 VD + IE G L+GPSGCGK+T LR +AG ED+ G+I + V+ L P+ Sbjct: 19 VDGIGFHIEAGVIACLLGPSGCGKTTLLRCIAGFEDIAAGSIALDGELVSRPGFKLAPEQ 78 Query: 77 RDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKAL 136 R I MVFQ+YAL+PH+TVADN+ F LK G E +Q+V ++ L ++ P L Sbjct: 79 RRIGMVFQDYALFPHLTVADNIAFGLKTKG---GERQQRVAAMLDLVGLAGQGEKYPHEL 135 Query: 137 SGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQ 196 SGGQ+QRVA+ RA+ P++ L+DEP SNLD LR ++ + ++ G T + VTHDQ Sbjct: 136 SGGQQQRVALARALAPAPRLVLLDEPFSNLDVDLRERLSLEVREILKKAGTTAILVTHDQ 195 Query: 197 VEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIG 237 EA M D + V+ +G +QQ D+P N+Y +PAN FVA F+G Sbjct: 196 HEAFAMADEIGVMHEGRIQQWDTPYNLYHQPANRFVADFVG 236 Lambda K H 0.317 0.135 0.379 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: 339 Number of extensions: 17 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: 377 Length of database: 356 Length adjustment: 30 Effective length of query: 347 Effective length of database: 326 Effective search space: 113122 Effective search space used: 113122 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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