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 7026373 Shewana3_3515 ABC transporter related (RefSeq)
Query= TCDB::P96483 (377 letters) >FitnessBrowser__ANA3:7026373 Length = 349 Score = 174 bits (442), Expect = 3e-48 Identities = 90/232 (38%), Positives = 146/232 (62%), Gaps = 8/232 (3%) Query: 24 LDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVT----HLPPKDRDI 79 LD+ + GE L L+GPSGCGK+T LR +AGL+ ++ G I+I + V+ +P + R I Sbjct: 23 LDLTLAQGEILALLGPSGCGKTTLLRAVAGLQAISQGEIQINGKTVSGAGQFVPSEQRGI 82 Query: 80 AMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKALSGG 139 M+FQ+YAL+PH+TVA+N+ F +A + A+ + ++++ ++ L R P LSGG Sbjct: 83 GMIFQDYALFPHLTVAENILFG--VAKLTPAQRKARLDDMLALVKLEGLAKRYPHELSGG 140 Query: 140 QRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVEA 199 Q+QRV++ RA+ EPQ+ L+DEP SN+DA++R S +I S+ ++ ++ V+VTH + EA Sbjct: 141 QQQRVSIARALAYEPQLLLLDEPFSNIDAQVRHSMMAEIRSILKQRNVSAVFVTHSKDEA 200 Query: 200 MTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDG 251 D +A+ G++ Q N+Y P + +VA F+GS N + + DG Sbjct: 201 FVFADTLAIFNQGVIVQHGRAENLYAAPNSRYVADFLGSG--NYLPAEVIDG 250 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: 267 Number of extensions: 13 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: 349 Length adjustment: 29 Effective length of query: 348 Effective length of database: 320 Effective search space: 111360 Effective search space used: 111360 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