Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate BWI76_RS14600 BWI76_RS14600 ABC transporter ATP-binding protein
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Koxy:BWI76_RS14600 Length = 260 Score = 190 bits (482), Expect = 3e-53 Identities = 96/237 (40%), Positives = 157/237 (66%), Gaps = 4/237 (1%) Query: 5 LEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFE 64 +E+ ++ K++G++++L GV++E+ GEV+ L+GDNGAGKSTL K++SG P G + + Sbjct: 11 VEMINITKTYGSIRSLRGVNLELAPGEVLGLVGDNGAGKSTLTKVLSGAVIPSGGTIRID 70 Query: 65 GKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKI----FLNKKKMMEE 120 G++ F +P D+R IE +YQDL+L + + N+F+ RE + FL++ KM + Sbjct: 71 GEQQQFANPADSRRCHIEMVYQDLSLCDTVDVAGNLFMGREPMKSVLGIPFLDEAKMHAD 130 Query: 121 SKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKV 180 ++++L L I IPD + V NLSGGQRQA+A+ARA F K+++MDEPTAAL+V E V Sbjct: 131 AREMLKGLGISIPDTRLLVRNLSGGQRQAIAIARAAAFDPKVLIMDEPTAALAVAEVEAV 190 Query: 181 LELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVM 237 LEL R + +G+ V++ITH + + V DRI V+ G + ++ +T++ +I ++ Sbjct: 191 LELIRRVSARGVSVILITHRLQDLFLVCDRIMVMYEGTNVADRRVADTSLSDIVNLI 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: 134 Number of extensions: 4 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: 251 Length of database: 260 Length adjustment: 24 Effective length of query: 227 Effective length of database: 236 Effective search space: 53572 Effective search space used: 53572 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