Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate GFF2490 PS417_12700 ABC transporter ATP-binding protein
Query= TCDB::Q9R9Q4 (342 letters) >FitnessBrowser__WCS417:GFF2490 Length = 367 Score = 357 bits (916), Expect = e-103 Identities = 191/369 (51%), Positives = 251/369 (68%), Gaps = 29/369 (7%) Query: 1 MAELQLRDIRKSFGAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTL 60 MA L++++++K F F +IKG+ +E+ EF+VFVGPSGCGKSTLLRLIAGLEE++ GT+ Sbjct: 1 MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTI 60 Query: 61 AFDGQIVNQLTPSRRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAEM 120 DG+ + ++TP++R +AMVFQ+YALYPHM+V +NM+F + LAG DK+ +V AA + Sbjct: 61 ELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKKLVESKVSEAARI 120 Query: 121 LQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLH 180 L+L P LER P+QLSGGQRQRVAIGRAIVR+PK+FLFDEPLSNLDAALRV RLE+A+LH Sbjct: 121 LELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLH 180 Query: 181 RSMHKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPKM 240 + + + TMIYVTHDQVEAMTLAD++ VL G +EQ+G+PLELY P ++FVAGF+G+PKM Sbjct: 181 KEL-QATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKM 239 Query: 241 NF--------------------------LSGAFAEPYKADTIGIRAEHLEIDEQG-GEWS 273 F LSGA A T+GIR EHLEI G + Sbjct: 240 GFLKGKVTRVESQSCEVQLDAGTLINLPLSGATLSVGSAVTLGIRPEHLEIASPGQTTLT 299 Query: 274 GTVIHSEMLGSDSYIYLDIGTGEPVIVRESGIAKHQPGQTIRISPAAGQVHRFDAGGRAL 333 T E LGSD++ ++ GEP+ +R G Q G+T+ + H FD G A+ Sbjct: 300 VTADVGERLGSDTFCHVITANGEPLTMRIRGDMASQYGETLHLHLDPAHCHLFDTDGVAV 359 Query: 334 GRMQMRGAA 342 R +R AA Sbjct: 360 AR-PLRAAA 367 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: 11 Number of successful extensions: 4 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: 367 Length adjustment: 29 Effective length of query: 313 Effective length of database: 338 Effective search space: 105794 Effective search space used: 105794 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