Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate WP_011653612.1 RL_RS21730 ABC transporter ATP-binding protein
Query= TCDB::Q9R9Q4 (342 letters) >NCBI__GCF_000009265.1:WP_011653612.1 Length = 332 Score = 378 bits (970), Expect = e-109 Identities = 187/333 (56%), Positives = 246/333 (73%), Gaps = 1/333 (0%) Query: 1 MAELQLRDIRKSFGAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTL 60 M + L+ + K FG VI + ++IK GEF+VFVGPSGCGKSTLLRLIAGLE+++ G + Sbjct: 1 MGSITLQKVSKVFGEAKVIPSIDLDIKDGEFVVFVGPSGCGKSTLLRLIAGLEDVSGGKI 60 Query: 61 AFDGQIVNQLTPSRRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAEM 120 DG+ + PS RG+AMVFQSYALYPHM+V N+AF +++AG DK + ++V AA + Sbjct: 61 VIDGRDATEKAPSERGLAMVFQSYALYPHMSVRNNIAFPLKMAGVDKAEIDRKVSDAARV 120 Query: 121 LQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLH 180 L LT YLER PRQLSGGQRQRVAIGRAIVR P FLFDEPLSNLDAALRV RLEI++LH Sbjct: 121 LNLTDYLERKPRQLSGGQRQRVAIGRAIVRQPSAFLFDEPLSNLDAALRVNMRLEISELH 180 Query: 181 RSMHKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPKM 240 + + KTTM+YVTHDQVEAMT+AD+I VL G +EQ+G+PLELY P ++FVAGFIGSP+M Sbjct: 181 QQL-KTTMVYVTHDQVEAMTMADKIVVLNRGNIEQVGSPLELYSRPRNLFVAGFIGSPRM 239 Query: 241 NFLSGAFAEPYKADTIGIRAEHLEIDEQGGEWSGTVIHSEMLGSDSYIYLDIGTGEPVIV 300 NF++G A A TIG+R EH+ + + GEW G V+ +E LGSD+++++D + Sbjct: 240 NFITGQHAAALNAHTIGVRPEHVLLSMESGEWKGRVVVAEHLGSDTFLHIDADGIGMLTA 299 Query: 301 RESGIAKHQPGQTIRISPAAGQVHRFDAGGRAL 333 R SG + G T+ ++P ++H+F+ GG A+ Sbjct: 300 RGSGDFAAKAGDTVFLTPDRSRIHKFNEGGLAI 332 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: 348 Number of extensions: 9 Number of successful extensions: 2 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: 332 Length adjustment: 28 Effective length of query: 314 Effective length of database: 304 Effective search space: 95456 Effective search space used: 95456 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