Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate Ac3H11_2941 Various polyols ABC transporter, ATP-binding component
Query= TCDB::Q9R9Q4 (342 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2941 Length = 350 Score = 342 bits (878), Expect = 6e-99 Identities = 191/346 (55%), Positives = 237/346 (68%), Gaps = 14/346 (4%) Query: 1 MAELQLRDIRKSFGAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTL 60 MA LQLR I K FG IKG+ + I+ GEF+VFVGPSGCGKSTLLRLIAGLE I G+L Sbjct: 1 MAYLQLRGIEKFFGEHRAIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGSL 60 Query: 61 AFDGQIVNQLTPSRRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAEM 120 DG+ + S+R +AMVFQSYALYPHM+VYENM+F ++LA DKQ ++V+ AA + Sbjct: 61 MLDGRDITDQPSSKRDLAMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAARI 120 Query: 121 LQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLH 180 L LT YL+R P++LSGGQRQRVAIGRAIVR PKVFLFDEPLSNLDAALR TR+EIAKLH Sbjct: 121 LNLTQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAKLH 180 Query: 181 RSMHKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPKM 240 R + TT IYVTHDQVEAMTLADR+ VLRDG++EQ+GTPLELY+ P + FVA FIG+P+M Sbjct: 181 RDLGATT-IYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIGTPQM 239 Query: 241 NFL----------SGAFAEPYKA--DTIGIRAEHLEIDEQGG-EWSGTVIHSEMLGSDSY 287 N + A A P A IG+R E++ + G G V E LG+++ Sbjct: 240 NVVPVDKLPQPVQQQAPAAPAGAAVGAIGLRPENITVRTTGATPVGGQVDLIEALGAETL 299 Query: 288 IYLDIGTGEPVIVRESGIAKHQPGQTIRISPAAGQVHRFDAGGRAL 333 IY+ G + R++ + G + + A Q H FD GR + Sbjct: 300 IYVTTPGGAQFVSRQNDRTDLRVGDAVSLDIDASQAHWFDTAGRVV 345 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: 390 Number of extensions: 17 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: 350 Length adjustment: 29 Effective length of query: 313 Effective length of database: 321 Effective search space: 100473 Effective search space used: 100473 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