Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate 8502259 DvMF_2969 ABC transporter related (RefSeq)
Query= TCDB::Q9R9Q4 (342 letters) >FitnessBrowser__Miya:8502259 Length = 418 Score = 203 bits (516), Expect = 7e-57 Identities = 107/248 (43%), Positives = 152/248 (61%), Gaps = 3/248 (1%) Query: 2 AELQLRDIRKSFGAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTLA 61 A+L + + K F F + VS E++ G F +GPSGCGK+TLLR+IAG E SG +A Sbjct: 27 ADLSVTRLVKRFEKFTAVNDVSFEVEQGRFFSILGPSGCGKTTLLRMIAGFESPDSGVIA 86 Query: 62 FDGQIVNQLTPSRRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAEML 121 G+ + + P+RR + ++FQ AL+P M+V EN+AFG++ G + +RV+ E + Sbjct: 87 IRGRDMAGIAPNRRPVNLIFQHLALFPMMSVAENVAFGLKRRGMAGGEISRRVQDVLERV 146 Query: 122 QLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLHR 181 L Y ++P QLSGGQ+QRVAI R +V +P V L DEPL LD LR ++E+ L Sbjct: 147 GLPGYGVKMPAQLSGGQKQRVAIARCLVLEPAVLLLDEPLGALDLKLREQMKVELKTLQA 206 Query: 182 SMHKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPKMN 241 + TT +Y+THDQ EA+ ++D + V+ G EQ+ TP LY P S FVAGF+G + N Sbjct: 207 EV-GTTFVYITHDQSEALVMSDHVAVMNAGRFEQVDTPRNLYRRPASAFVAGFVG--ETN 263 Query: 242 FLSGAFAE 249 SG E Sbjct: 264 VWSGTLEE 271 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: 349 Number of extensions: 15 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: 418 Length adjustment: 30 Effective length of query: 312 Effective length of database: 388 Effective search space: 121056 Effective search space used: 121056 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: 50 (23.9 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