Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate WP_085638891.1 MGEO_RS13900 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::Q9R9Q4 (342 letters) >NCBI__GCF_002115805.1:WP_085638891.1 Length = 362 Score = 341 bits (875), Expect = 1e-98 Identities = 190/362 (52%), Positives = 241/362 (66%), Gaps = 27/362 (7%) Query: 1 MAELQLRDIRKSF-GAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGT 59 MA L+L ++ K++ GA +V+ ++++I+ GE +VFVGPSGCGKSTLLR+IAGLE+IT GT Sbjct: 1 MANLKLTNVEKTYAGAVNVLNNINLDIEKGELIVFVGPSGCGKSTLLRMIAGLEKITGGT 60 Query: 60 LAFDGQIVNQLTPSRRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAE 119 L DGQ+VN + P+ RGIAMVFQSYALYPHMTV ENM+F +++A K + + VE AA+ Sbjct: 61 LEIDGQVVNDMPPAMRGIAMVFQSYALYPHMTVRENMSFALKIAKKPQSEIDAAVERAAK 120 Query: 120 MLQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKL 179 MLQL PYL+RLP+ LSGGQRQRVAIGR+IVRDPKV+LFDEPLSNLDAALRVATR+EIA+L Sbjct: 121 MLQLDPYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRIEIAQL 180 Query: 180 HRSMHKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPK 239 M ++TMIYVTHDQVEAMTLA RI VL + + Q+G PLELYE PNS FVA FIGSP Sbjct: 181 KEQMPESTMIYVTHDQVEAMTLASRIVVLANKGIAQVGAPLELYERPNSEFVAQFIGSPS 240 Query: 240 MNFLSGAFAEPYKADT-------------------------IGIRAEHLEIDEQGGEWSG 274 MN L G + T +G+R E + G Sbjct: 241 MNLLPGEIVGTGQQTTVKMDGGGVAVSDYPTTDADMGLKVNVGVRPEDFVGTSGDHIFEG 300 Query: 275 TVIHSEMLGSDSYIYLD-IGTGEPVIVRESGIAKHQPGQTIRISPAAGQVHRFDAGGRAL 333 V +E LG + +Y + G G VI + GI G+T+++ + +VH F G L Sbjct: 301 RVEITEALGEVTLLYFEKQGDGHAVIGKLPGIHAELRGKTVKLGASPDKVHIFHNGTSLL 360 Query: 334 GR 335 R Sbjct: 361 YR 362 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: 377 Number of extensions: 15 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: 362 Length adjustment: 29 Effective length of query: 313 Effective length of database: 333 Effective search space: 104229 Effective search space used: 104229 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