Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate WP_106710281.1 CU102_RS06970 ABC transporter ATP-binding protein
Query= TCDB::Q9R9Q4 (342 letters) >NCBI__GCF_003010955.1:WP_106710281.1 Length = 333 Score = 388 bits (996), Expect = e-112 Identities = 194/333 (58%), Positives = 249/333 (74%), Gaps = 2/333 (0%) Query: 1 MAELQLRDIRKSFGAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTL 60 M L++ +IRKSFG DV+KG+ +E+K GEF++FVGPSGCGKSTLLR+IAGLE+ TSG + Sbjct: 1 MGSLKIENIRKSFGHVDVLKGIDLEVKDGEFVIFVGPSGCGKSTLLRVIAGLEDATSGDI 60 Query: 61 AFDGQIVNQLTPSRRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAEM 120 DG+ VN P++RGIAMVFQ+YALYPH++V +NM G++ AGK + ++R A+ M Sbjct: 61 LIDGKKVNNTPPAKRGIAMVFQTYALYPHLSVRDNMGLGLKQAGKPADEIKERTGIASSM 120 Query: 121 LQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLH 180 L L YLER P +LSGGQRQRVAIGRAIVR+P++FLFDEPLSNLDAALRV TRLEIA+LH Sbjct: 121 LSLDEYLERRPAELSGGQRQRVAIGRAIVREPQLFLFDEPLSNLDAALRVNTRLEIARLH 180 Query: 181 RSMHKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPKM 240 R + K TMIYVTHDQVEAMTLAD+I VL G +EQ+G+P+ELY P ++FVAGFIGSP+M Sbjct: 181 RQL-KATMIYVTHDQVEAMTLADKIVVLNKGKIEQVGSPMELYNAPQTIFVAGFIGSPQM 239 Query: 241 NFLSGAFAEPYKADTIGIRAEHLEIDEQGGEWSGTVIHSEMLGSDSYIYLDIGTGEPVIV 300 N + A A TIGIR EH+++ + GEW G+VIH E LG+D+ IYL G P+ V Sbjct: 240 NLIDAAKLGQSGAKTIGIRPEHIQVSKTSGEWKGSVIHVEHLGADTIIYLQTDFG-PLTV 298 Query: 301 RESGIAKHQPGQTIRISPAAGQVHRFDAGGRAL 333 R G + + +P AG+ +RFD G+ + Sbjct: 299 RLFGEHNYDVDGVLYATPDAGRTYRFDNDGQVI 331 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: 360 Number of extensions: 11 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: 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 24 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