Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate WP_086511012.1 BZY95_RS16625 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::Q9R9Q4 (342 letters) >NCBI__GCF_002151265.1:WP_086511012.1 Length = 346 Score = 344 bits (882), Expect = 2e-99 Identities = 183/334 (54%), Positives = 232/334 (69%), Gaps = 2/334 (0%) Query: 1 MAELQLRDIRKSF-GAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGT 59 MA++ L DI K+F G VI +++ I+ G F V VGPSGCGKSTLLR+IAGLE +T G Sbjct: 1 MADVTLVDIEKTFRGKTTVIPNLNLRIEDGSFTVLVGPSGCGKSTLLRMIAGLETVTRGA 60 Query: 60 LAFDGQIVNQLTPSRRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAE 119 ++ G+ V PS R IAMVFQSYALYPHMTV N+ FGM+LA ++ +V AA Sbjct: 61 ISIGGRDVTTAEPSERNIAMVFQSYALYPHMTVARNIDFGMRLAKVPTEERMAKVAEAAR 120 Query: 120 MLQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKL 179 +L L LER P +LSGGQRQRVAIGRAIVR+P VFLFDEPLSNLDAALR R+E+A+L Sbjct: 121 LLNLEELLERKPAELSGGQRQRVAIGRAIVRNPGVFLFDEPLSNLDAALRNRMRVELAEL 180 Query: 180 HRSMHKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPK 239 H+ + TMIYVTHDQVEAMTLAD I V+ G +EQ+GTP+ LY+ P ++FVAGFIGSPK Sbjct: 181 HQRL-DATMIYVTHDQVEAMTLADCIVVMNAGQIEQVGTPMNLYQRPETLFVAGFIGSPK 239 Query: 240 MNFLSGAFAEPYKADTIGIRAEHLEIDEQGGEWSGTVIHSEMLGSDSYIYLDIGTGEPVI 299 MN + G A+ + A T+GIR EHLE+ + GEW V EMLG+D++ Y+D P+ Sbjct: 240 MNLIEGEVAKAHGATTLGIRPEHLEVSHEAGEWRTRVRVVEMLGADAFAYVDSDATGPLT 299 Query: 300 VRESGIAKHQPGQTIRISPAAGQVHRFDAGGRAL 333 VR G A+ + G + ++P +H F GR L Sbjct: 300 VRLPGDAEVRSGDILYLTPRYELLHAFGIDGRRL 333 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: 351 Number of extensions: 17 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: 346 Length adjustment: 29 Effective length of query: 313 Effective length of database: 317 Effective search space: 99221 Effective search space used: 99221 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