Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate SM_b20904 SM_b20904 sugar uptake ABC transporter ATP-binding protein
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Smeli:SM_b20904 Length = 261 Score = 190 bits (483), Expect = 2e-53 Identities = 100/243 (41%), Positives = 161/243 (66%), Gaps = 4/243 (1%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 L+E++++ SFG + A+D S+++ GEVVALLG NGAGKSTLIKI+SG +K D G+++ Sbjct: 8 LVEMKNISISFGGIHAVDDASVDLYPGEVVALLGHNGAGKSTLIKILSGAYKRDAGEILI 67 Query: 64 EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREV-TNKIFLNKKKMMEESK 122 G+ N+P DA+ GIETIYQ LA+ ++ N++L RE+ T L+ M +++ Sbjct: 68 NGEPAEINNPRDAKKYGIETIYQTLAVADNVDAAANLYLGRELRTPWGTLDDVAMEAKAR 127 Query: 123 KLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLE 182 +++ L V+ LSGGQRQ+VA+ARA+ F A++++MDEPTAAL E +V E Sbjct: 128 EVMGRLNPNFQRFKEPVKALSGGQRQSVAIARAILFDARILIMDEPTAALGPQETAQVGE 187 Query: 183 LARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMTSFAL 242 L + LK++G+G+ +I+H+I +++ADR+ V+ G+++ H + E+ + EV+ + Sbjct: 188 LIKQLKREGIGIFLISHDIHDVFDLADRVSVMKNGQVVGHARTEDVTKD---EVLGMIIM 244 Query: 243 GKV 245 GKV Sbjct: 245 GKV 247 Lambda K H 0.318 0.137 0.371 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: 148 Number of extensions: 8 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: 251 Length of database: 261 Length adjustment: 24 Effective length of query: 227 Effective length of database: 237 Effective search space: 53799 Effective search space used: 53799 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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