Align TreU, component of Trehalose porter (characterized)
to candidate WP_110804034.1 C8J30_RS01980 carbohydrate ABC transporter permease
Query= TCDB::Q97ZC1 (267 letters) >NCBI__GCF_003217355.1:WP_110804034.1 Length = 382 Score = 81.6 bits (200), Expect = 2e-20 Identities = 70/243 (28%), Positives = 114/243 (46%), Gaps = 27/243 (11%) Query: 41 SLLPVSLTLNNLLTALQGTAFIDPFIKSLETATLVGIITIALAIPAGYGLS--RLP-RAI 97 ++ P LT N + F+ ++ +I I +A A Y L+ R P RA+ Sbjct: 150 TVAPPRLTTGNYARVITAEGIGRAFLNTMTVTIPATVIPILIAAFAAYALAWMRFPGRAL 209 Query: 98 AYSIIILLLVTNMMPAIVIGIPIAVDFLKLH----LFESVVGLALAQTLITLPLATFILQ 153 + I+ LLV + A++ LKLH L +S +G+ LA T LPLA ++L+ Sbjct: 210 LVATIVGLLVVPLQLALI-------PLLKLHNQIGLNQSYLGIWLAHTGFGLPLAIYLLR 262 Query: 154 GTFSSIPIDLEHQARVDGANLFNRLFSVLLPLAAPGIAAAFLISWMFSWDEFTYAILLIP 213 +P ++ ARVDGA F ++LPL+ P +A+ + +++ W++ A + + Sbjct: 263 NYMVGLPREIIESARVDGATEFQIFRRIVLPLSFPALASFAIFQFLWVWNDLLVATVFL- 321 Query: 214 YHSTLPVTIYQDVTRG---------NLLAGIAFSLIFTLPVIILTFALQKYLRGEYLAGG 264 + + R +LA AF I +P+I+ FALQKYL LAG Sbjct: 322 -GNATDTQVMTGALRALLGSRGGDWEILAASAFVSI-AVPLIVF-FALQKYLVRGLLAGS 378 Query: 265 IKG 267 +KG Sbjct: 379 VKG 381 Lambda K H 0.330 0.146 0.431 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: 270 Number of extensions: 17 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: 267 Length of database: 382 Length adjustment: 28 Effective length of query: 239 Effective length of database: 354 Effective search space: 84606 Effective search space used: 84606 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 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