Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate WP_011307343.1 MBAR_RS12630 glycine betaine/L-proline ABC transporter ATP-binding protein
Query= TCDB::Q9R9Q4 (342 letters) >NCBI__GCF_000195895.1:WP_011307343.1 Length = 506 Score = 157 bits (397), Expect = 6e-43 Identities = 88/223 (39%), Positives = 131/223 (58%), Gaps = 7/223 (3%) Query: 19 IKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTLAFDGQIVNQLTPS----- 73 + V+ E+ GE V +G SG GKSTLLR + L E T+G + DGQ + Q+ Sbjct: 46 LNNVNFEVYEGEIFVIMGLSGSGKSTLLRCLNRLIEPTAGEILIDGQNITQMNAEELRDV 105 Query: 74 -RRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAEMLQLTPYLERLPR 132 R I MVFQ++AL PH V +N+A+G+++ G K++ + A+ E + L Y Sbjct: 106 RRTRIGMVFQNFALLPHKIVLDNVAYGLEIQGIPKEERYSKALASIETVGLKGYEHSRIN 165 Query: 133 QLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLHRSMHKTTMIYVT 192 QLSGG +QRV + RA+ DP++ L DE S LD +R + E+ L + K T+I+V+ Sbjct: 166 QLSGGMKQRVGLARALANDPEILLMDEAFSALDPLIRNEMQDELIALEDRVQK-TIIFVS 224 Query: 193 HDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFI 235 HD EA+ L DRI +++DG V QIGTP E+ P + +V+ F+ Sbjct: 225 HDLDEALKLGDRIAIMKDGEVVQIGTPEEILTEPANSYVSKFV 267 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: 352 Number of extensions: 18 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: 342 Length of database: 506 Length adjustment: 31 Effective length of query: 311 Effective length of database: 475 Effective search space: 147725 Effective search space used: 147725 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: 50 (23.9 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