Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate 3608624 Dshi_2017 ABC transporter related (RefSeq)
Query= TCDB::Q9R9Q4 (342 letters) >FitnessBrowser__Dino:3608624 Length = 333 Score = 326 bits (836), Expect = 5e-94 Identities = 171/307 (55%), Positives = 218/307 (71%), Gaps = 3/307 (0%) Query: 1 MAELQLRDIRKSFGAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTL 60 MA L L +++KSFG DVI GVS+++ GEF+V VGPSGCGKSTLLR++AGLE ++SG + Sbjct: 1 MATLTLDNVKKSFGKTDVIHGVSIDVTEGEFIVIVGPSGCGKSTLLRMVAGLETVSSGEV 60 Query: 61 AFDGQIVNQLTPSRRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAEM 120 DG++VN L P R IAMVFQ+YALYPHM+V++NMA+G+++A K + RV AA++ Sbjct: 61 RIDGRVVNTLEPMDRDIAMVFQNYALYPHMSVFDNMAYGLKIAKVPKAEIADRVAVAAKL 120 Query: 121 LQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLH 180 LQL PYL R P++LSGGQRQRVA+GRAIVR P VFLFDEPLSNLDA LRV RLEI L Sbjct: 121 LQLEPYLGRKPKELSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQMRLEIKALQ 180 Query: 181 RSMHKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPKM 240 R + T +YVTHDQVEAMTLADR+ V+ G+ +QIG PLE+Y P + FVAGFIGSP Sbjct: 181 REL-GVTSLYVTHDQVEAMTLADRMIVMNGGVADQIGAPLEVYANPQTAFVAGFIGSPPT 239 Query: 241 NFLSGAFAEPYKA-DTIGIRAEHLEIDEQGGEWSGTVIHSEMLGSDSYIYLDIGTGEPVI 299 NFL A +GIR EHL + Q G V ++E LG+++ ++L G + Sbjct: 240 NFLPADMVRAGPAGQQVGIRPEHLRVAPQ-GRLEAHVAYAEALGAETLLHLRASQGTTLT 298 Query: 300 VRESGIA 306 VR+ A Sbjct: 299 VRQDAAA 305 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: 343 Number of extensions: 12 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: 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