Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate N515DRAFT_1740 N515DRAFT_1740 putative ABC transport system ATP-binding protein
Query= TCDB::Q9R9Q4 (342 letters) >FitnessBrowser__Dyella79:N515DRAFT_1740 Length = 234 Score = 131 bits (329), Expect = 2e-35 Identities = 87/229 (37%), Positives = 122/229 (53%), Gaps = 15/229 (6%) Query: 4 LQLRDIRKSF----GAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGT 59 L+ RD+ KS G D+++GVS++++ GE VG SG GK+TLL L+AGL+ + G Sbjct: 9 LEARDVSKSVRGPEGQLDILRGVSLQVRDGESFAIVGASGSGKTTLLGLLAGLDVPSGGH 68 Query: 60 LAFDGQIVNQLTPS------RRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKR 113 + DG + L RR + VFQS+ L P +T EN+ ++L G+D R R Sbjct: 69 VGLDGHALESLDEEARADLRRRLVGFVFQSFHLLPALTAEENVMLPLELEGRD--DARPR 126 Query: 114 VEAAAEMLQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATR 173 A E + L P QLSGG++QRVAI RA V P++ DEP NLD Sbjct: 127 AREALEAVGLGARRRHYPAQLSGGEQQRVAIARAFVHGPRLLFADEPTGNLDQRTGHHVS 186 Query: 174 LEIAKLHRSMHKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLEL 222 + L+R H+TT++ VTHD + A R+ L +G V G P EL Sbjct: 187 DLLFALNRD-HRTTLVLVTHDPLLAERCERRV-ELHEGRVIARG-PAEL 232 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: 190 Number of extensions: 11 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 342 Length of database: 234 Length adjustment: 26 Effective length of query: 316 Effective length of database: 208 Effective search space: 65728 Effective search space used: 65728 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: 47 (22.7 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