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_078717009.1 B5D49_RS06865 spermidine/putrescine ABC transporter ATP-binding protein PotA
Query= TCDB::P96483 (377 letters) >NCBI__GCF_900167125.1:WP_078717009.1 Length = 370 Score = 226 bits (576), Expect = 8e-64 Identities = 109/226 (48%), Positives = 157/226 (69%) Query: 28 IEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRDIAMVFQNYA 87 I GEFL ++GPSGCGK+T LR+LAG E + G I + R + +PP R + VFQ+YA Sbjct: 30 IRHGEFLTILGPSGCGKTTLLRLLAGFESPSSGEIILDGRSMRDVPPDGRRVNTVFQSYA 89 Query: 88 LYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKALSGGQRQRVAMG 147 L+PHM+V DN+ F L+++G+PK EI ++V +A +++ L R+P +LSGGQ+QRVA+ Sbjct: 90 LFPHMSVFDNVAFGLRMSGIPKVEIGERVAKALRMVGLAGQAGRRPTSLSGGQQQRVAIA 149 Query: 148 RAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVEAMTMGDRVA 207 RA+V P V L+DEPLS LD KLRV RT++ L+R +GIT ++VTHDQ EA +M DRV Sbjct: 150 RAVVNRPLVLLLDEPLSALDYKLRVQMRTELKQLRREMGITFIFVTHDQEEAFSMSDRVV 209 Query: 208 VLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGGV 253 V+ +G + QV +P +Y++P N+FVA F+G + +DGG+ Sbjct: 210 VMNEGCVAQVGTPVEVYEQPVNMFVARFVGETNVFEGVAGQSDGGI 255 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: 374 Number of extensions: 17 Number of successful extensions: 1 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: 370 Length adjustment: 30 Effective length of query: 347 Effective length of database: 340 Effective search space: 117980 Effective search space used: 117980 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: 50 (23.9 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