Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_037150766.1 RHSP_RS09200 sugar ABC transporter ATP-binding protein
Query= uniprot:P0DTT6 (251 letters) >NCBI__GCF_000359745.1:WP_037150766.1 Length = 273 Score = 197 bits (502), Expect = 1e-55 Identities = 105/237 (44%), Positives = 159/237 (67%), Gaps = 6/237 (2%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 +L ++ + K FGAV AL ++++++ GEVVAL+GDNGAGKSTL+K+++G H+P G + F Sbjct: 15 VLSLKGISKHFGAVSALTDINLDVHAGEVVALVGDNGAGKSTLVKVLAGVHQPSSGTITF 74 Query: 64 EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKK 123 GK+V + P A LGI T++QDLAL +L + NIFL RE+ + I L++ M + Sbjct: 75 RGKQVTLSDPATALDLGIATVFQDLALCENLDVVANIFLGREL-SPIKLDETAMEVRAWT 133 Query: 124 LLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLEL 183 LL+ L RIP + + + +LSGGQRQ VA+AR++ K+I++DEPTAAL V + +VL L Sbjct: 134 LLNELAARIPSVRIPIASLSGGQRQTVAIARSLLLEPKLIMLDEPTAALGVAQTAEVLNL 193 Query: 184 ARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKI--IFHKKKEETNVEEITEVMT 238 ++ KGLGV++I+HN+ VADRI VL G+ IF+ +T+ +E+ +T Sbjct: 194 IERVRDKGLGVIMISHNMEDVRAVADRIVVLRLGRNNGIFY---PDTSNQELVSAIT 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: 162 Number of extensions: 7 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: 273 Length adjustment: 25 Effective length of query: 226 Effective length of database: 248 Effective search space: 56048 Effective search space used: 56048 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 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