Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate 350994 BT1466 ABC transporter ATP-binding protein (NCBI ptt file)
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Btheta:350994 Length = 238 Score = 128 bits (321), Expect = 2e-34 Identities = 79/214 (36%), Positives = 123/214 (57%), Gaps = 11/214 (5%) Query: 16 TVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIGG---DHMNYR-- 70 T A+++++L ++ EF+ ++GPSGCGKST L +L L++PTSG + G D MN Sbjct: 18 TKALNEVTLHVEQGEFVAIMGPSGCGKSTLLNILGTLDSPTSGSYFFEGKQVDKMNENQL 77 Query: 71 -VPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLGIADLLD 129 + ++ +FQ + L +TV +N+ L G +A+R E+V +V E + + + Sbjct: 78 TALRKNNLGFIFQSFNLIDELTVYENVELPLVYM-GIKTAQRKEKVNKVLEKVNLLHRAN 136 Query: 130 RKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQLAVTTV 189 P +LSGGQQQRVA+ RA+V D ++ L DEP NLD+ E+ L L Q T + Sbjct: 137 HYPQQLSGGQQQRVAIARAVVTDCKLLLADEPTGNLDSVNGVEVMELLSELNRQ-GTTII 195 Query: 190 YVTHNQTEAMTMADRIAVMDDGEL--QQVASPFE 221 VTH+Q +A T A RI + DG++ + + P E Sbjct: 196 IVTHSQRDA-TYAHRIIRLLDGQIVSENINRPLE 228 Lambda K H 0.317 0.135 0.386 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: 173 Number of extensions: 13 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: 383 Length of database: 238 Length adjustment: 27 Effective length of query: 356 Effective length of database: 211 Effective search space: 75116 Effective search space used: 75116 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 (21.6 bits) S2: 48 (23.1 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