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 WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein
Query= TCDB::P96483 (377 letters) >NCBI__GCF_000016765.1:WP_041378948.1 Length = 252 Score = 147 bits (371), Expect = 3e-40 Identities = 82/221 (37%), Positives = 122/221 (55%), Gaps = 5/221 (2%) Query: 4 VTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIR 63 ++FD + Y G + +D + + IE G F+ LVG SG GK+T L+ + L +++ G I Sbjct: 2 ISFDHVGKHYAG--RHVLDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIA 59 Query: 64 IGDRDVTHLPPKD--RDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAK 121 I RDV P + R I VFQ L+PHM+VA+N+ ++ GVP+ E +V E Sbjct: 60 IEGRDVAAQPVAELRRRIGYVFQGIGLFPHMSVAENVALVPRLQGVPREERAARVAELLD 119 Query: 122 ILDL-TQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180 ++ L + +R+P LSGGQ QRV RA+ P + LMDEP LD R + Sbjct: 120 LVALPADFAERRPAQLSGGQAQRVGFARALAARPAIMLMDEPFGALDPVTRDELGAAYRA 179 Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPR 221 L +G+T++ VTHD EA+ + DRV V+ +G + PR Sbjct: 180 LHEAMGLTSLIVTHDMAEALLLADRVIVIGEGRILADQPPR 220 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: 220 Number of extensions: 11 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: 252 Length adjustment: 27 Effective length of query: 350 Effective length of database: 225 Effective search space: 78750 Effective search space used: 78750 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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