Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate WP_090274680.1 BLU11_RS14815 polyamine ABC transporter ATP-binding protein
Query= TCDB::Q9R9Q4 (342 letters) >NCBI__GCF_900105005.1:WP_090274680.1 Length = 378 Score = 194 bits (494), Expect = 2e-54 Identities = 99/234 (42%), Positives = 148/234 (63%), Gaps = 1/234 (0%) Query: 4 LQLRDIRKSFGAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTLAFD 63 +++ + K F + V++ I GE +G SG GKSTLLR++AG E + G + D Sbjct: 21 VKIERVSKQFDDALAVDDVTLTINRGEIFALLGGSGSGKSTLLRILAGFETPSEGRVLLD 80 Query: 64 GQIVNQLTPSRRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAEMLQL 123 GQ + L P +R I M+FQSYAL+PHMTV +N+AFG++ + +RV +++ + Sbjct: 81 GQNITALPPHKRPINMMFQSYALFPHMTVEQNIAFGLKQDKLSNTEISERVAEMLKLVHM 140 Query: 124 TPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLHRSM 183 Y +R P QLSGGQRQRVA+ R++ + PK+ L DEP+ LD LR +LE+ ++ + Sbjct: 141 AKYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLELVEIIERV 200 Query: 184 HKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGS 237 T I VTHDQ EAMT+A RI ++ G + Q+GTP+++YE+P + VA F+GS Sbjct: 201 -GVTCIMVTHDQEEAMTMAQRIAIMDQGWIVQVGTPMDIYESPVNRHVAEFVGS 253 Lambda K H 0.321 0.138 0.396 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: 312 Number of extensions: 14 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: 342 Length of database: 378 Length adjustment: 29 Effective length of query: 313 Effective length of database: 349 Effective search space: 109237 Effective search space used: 109237 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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