Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate SMc01499 SMc01499 ATP-binding transport ABC transporter protein
Query= TCDB::Q9R9Q4 (342 letters) >FitnessBrowser__Smeli:SMc01499 Length = 333 Score = 377 bits (968), Expect = e-109 Identities = 189/333 (56%), Positives = 251/333 (75%), Gaps = 1/333 (0%) Query: 1 MAELQLRDIRKSFGAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTL 60 M + L+++ K FGA VI + ++I GEF+VFVGPSGCGKSTLLRLIAGLE+++ G + Sbjct: 1 MGSITLKNVSKVFGAHAVIPSIDLDITDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGEI 60 Query: 61 AFDGQIVNQLTPSRRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAEM 120 DG+ +L P+RRG++MVFQSYALYPHM+V N+AF +++AG+DK K+VE AA + Sbjct: 61 VIDGRNATELPPARRGLSMVFQSYALYPHMSVRSNIAFPLKMAGEDKASIDKKVEDAARV 120 Query: 121 LQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLH 180 L LT YL+R PRQLSGGQRQRVAIGRAIVR P+ FLFDEPLSNLDAALRV RLEI++LH Sbjct: 121 LNLTDYLDRKPRQLSGGQRQRVAIGRAIVRQPEAFLFDEPLSNLDAALRVNMRLEISQLH 180 Query: 181 RSMHKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPKM 240 + + KTTM+YVTHDQVEAMT+AD+I VL G +EQ+G+PL+LY P+++FVAGFIGSPKM Sbjct: 181 QQL-KTTMVYVTHDQVEAMTMADKIVVLNRGRIEQVGSPLDLYRRPDNLFVAGFIGSPKM 239 Query: 241 NFLSGAFAEPYKADTIGIRAEHLEIDEQGGEWSGTVIHSEMLGSDSYIYLDIGTGEPVIV 300 NF++GA A ++A TIGIR EH+ + + G W GTV +E LGSD++++++ + Sbjct: 240 NFVTGAPAAAHQAHTIGIRPEHIALSKDQGTWRGTVGVAEHLGSDTFLHVNADGIGTLTA 299 Query: 301 RESGIAKHQPGQTIRISPAAGQVHRFDAGGRAL 333 R G G + ++P A ++HRFD G A+ Sbjct: 300 RVGGDFAVTHGDQVYLTPDAERLHRFDEKGLAI 332 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: 353 Number of extensions: 13 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: 333 Length adjustment: 28 Effective length of query: 314 Effective length of database: 305 Effective search space: 95770 Effective search space used: 95770 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 17 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