Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate WP_013645165.1 METBO_RS07885 ABC transporter ATP-binding protein
Query= TCDB::Q9R9Q4 (342 letters) >NCBI__GCF_000191585.1:WP_013645165.1 Length = 230 Score = 123 bits (308), Expect = 5e-33 Identities = 82/210 (39%), Positives = 118/210 (56%), Gaps = 18/210 (8%) Query: 17 DVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTLAFDGQIVNQLTPSR-- 74 + ++G+++ + GEF+ +GPSG GKSTL+ LI L+ T G L DG+ ++ + S Sbjct: 22 NALRGLNITVDEGEFVSIMGPSGSGKSTLMNLIGCLDTPTEGELTIDGREISSMKESELT 81 Query: 75 ----RGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQ----QCRKRVEAAAEMLQLTPY 126 I +FQ++ L P ++V +N+ F M+ DK+ R R E E + L Sbjct: 82 KVRAEKIGFIFQTFNLLPALSVRDNVEFPMRNLSGDKKLNKSARRARAEECLECVGLGHR 141 Query: 127 LERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLHRSMHK- 185 L+ LP +LSGG+RQRVAI RA+V PK L DEP NLD + I KL ++ Sbjct: 142 LDHLPAKLSGGERQRVAIARALVNKPKFILADEPTGNLD----TESTENIMKLLHDINDM 197 Query: 186 -TTMIYVTHDQVEAMTLADRICVLRDGLVE 214 TT+I VTHD VE T RI +RDG++E Sbjct: 198 GTTVIMVTHD-VET-TENTRILRIRDGVIE 225 Score = 23.1 bits (48), Expect = 0.007 Identities = 12/40 (30%), Positives = 17/40 (42%) Query: 256 IGIRAEHLEIDEQGGEWSGTVIHSEMLGSDSYIYLDIGTG 295 +G R +HL GGE I ++ +I D TG Sbjct: 138 LGHRLDHLPAKLSGGERQRVAIARALVNKPKFILADEPTG 177 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: 160 Number of extensions: 10 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 342 Length of database: 230 Length adjustment: 26 Effective length of query: 316 Effective length of database: 204 Effective search space: 64464 Effective search space used: 64464 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 Apr 09 2024. 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