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_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein
Query= TCDB::P96483 (377 letters) >NCBI__GCF_000016765.1:WP_012048833.1 Length = 241 Score = 126 bits (316), Expect = 7e-34 Identities = 74/222 (33%), Positives = 119/222 (53%), Gaps = 6/222 (2%) Query: 20 AVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTH----LPPK 75 A+ + + + GE +V+ GPSG GKST +R + GLE + G IRIG+ +V L Sbjct: 16 ALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRIGEDEVRPDRRVLQRI 75 Query: 76 DRDIAMVFQNYALYPHMTVADNMGFA-LKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPK 134 + MVFQ++ L+PH+T+ +N A +K+ G+ + E + + + D+ P Sbjct: 76 RARVGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEALARELLERVRIADQADKYPA 135 Query: 135 ALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTH 194 LSGGQ+QR A+ RA+ +P++ L DEP S LDA++ V I GIT + VTH Sbjct: 136 QLSGGQQQRTAIARALAMQPEIILFDEPTSALDAEM-VKEVLDIMKALATEGITMLCVTH 194 Query: 195 DQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFI 236 + A + DR+ + G + + SPR+ + P + F+ Sbjct: 195 EMGFAREVADRIIFMDAGQIVETGSPRDFFTAPCHERTRAFL 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: 210 Number of extensions: 7 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: 377 Length of database: 241 Length adjustment: 27 Effective length of query: 350 Effective length of database: 214 Effective search space: 74900 Effective search space used: 74900 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