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 5210215 Shew_2658 ABC transporter-related protein (RefSeq)
Query= TCDB::P96483 (377 letters) >FitnessBrowser__PV4:5210215 Length = 227 Score = 141 bits (355), Expect = 2e-38 Identities = 83/221 (37%), Positives = 123/221 (55%), Gaps = 10/221 (4%) Query: 3 TVTFDKATRIY-PGSDKP--AVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNG 59 T+ T+IY P SD P AV LD+ I GEF+ ++GPSG GK+T L M+ G++ + Sbjct: 2 TIAIQALTKIYNPESDFPVAAVKSLDLTIAQGEFVAIMGPSGSGKTTLLNMIGGIDSPSS 61 Query: 60 GAIRIGDRDVTHLPPKD-----RD-IAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIR 113 GA+ I D+THL + RD + +FQ+Y+L P +T +N+ F +++ G +AE R Sbjct: 62 GAVFIDGEDITHLSEQALIAFRRDHVGFIFQDYSLLPVLTALENVEFVMQLQGHSEAECR 121 Query: 114 QKVEEAAKILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVS 173 + + L D+ P LSGGQ+QRVA+ RA+ P+ + DEP +NLDAK Sbjct: 122 DRAMALLAQVGLAAQQDKIPAKLSGGQQQRVAVARALAPRPRFVMADEPTANLDAKSTAE 181 Query: 174 TRTQIASLQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLL 214 + SL + G T ++ THD + RV V +DG L Sbjct: 182 LLDIMQSLNEQEGTTFIFSTHDP-RVIARAKRVIVFEDGRL 221 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: 190 Number of extensions: 6 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: 227 Length adjustment: 26 Effective length of query: 351 Effective length of database: 201 Effective search space: 70551 Effective search space used: 70551 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 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