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_011973701.1 MAEO_RS04980 ABC transporter ATP-binding protein
Query= TCDB::P96483 (377 letters) >NCBI__GCF_000017185.1:WP_011973701.1 Length = 258 Score = 137 bits (344), Expect = 4e-37 Identities = 75/209 (35%), Positives = 117/209 (55%), Gaps = 10/209 (4%) Query: 20 AVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRDI 79 AV+ ++ ++ EFL +VGPSGCGKST LRM+AGLE G + + + + D + Sbjct: 23 AVEDVNFSVNSNEFLSIVGPSGCGKSTLLRMIAGLEKPTSGTLIL---EGNKIEKPDAER 79 Query: 80 AMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKALSGG 139 MVFQ Y L P TV N+ L+I G+ K E + + K++ L ++ + P LSGG Sbjct: 80 GMVFQQYTLLPWKTVLGNVALGLEIKGMKKEERNKIAKNFIKLIGLEEFENSYPYELSGG 139 Query: 140 QRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVEA 199 +QRVA+ R + +P++ LMDEP LD + RV + ++ + + T V++TH EA Sbjct: 140 MQQRVAIARTLANDPKIVLMDEPFGALDTQTRVILQNELLKIWEKDKKTVVFITHSVEEA 199 Query: 200 MTMGDRVAV-------LKDGLLQQVDSPR 221 + + DRV + +KD + +D PR Sbjct: 200 VYLSDRVIIMSARPGKIKDIVNIDIDRPR 228 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: 208 Number of extensions: 7 Number of successful extensions: 2 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: 258 Length adjustment: 27 Effective length of query: 350 Effective length of database: 231 Effective search space: 80850 Effective search space used: 80850 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