Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate SMc01980 SMc01980 sugar transport system ATP-binding ABC transporter protein
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Smeli:SMc01980 Length = 355 Score = 286 bits (731), Expect = 8e-82 Identities = 165/367 (44%), Positives = 215/367 (58%), Gaps = 21/367 (5%) Query: 1 MGQIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDI 60 M I + ++ K +G + D+ L I D EF+VLVGPSGCGKST LRM+AGLE+ T G+I Sbjct: 1 MASIDIANIKKSYGTHPVLHDVDLKISDGEFVVLVGPSGCGKSTLLRMIAGLESVTGGEI 60 Query: 61 YIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVE-VA 119 I G +N P++RDIAMVFQ YALYPHM+V +N+ + L + T+ +R VV A Sbjct: 61 RIAGRRVNELAPKDRDIAMVFQSYALYPHMSVARNMSYSLRLRK--TAKDRITTVVAGAA 118 Query: 120 ETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQN 179 LG+ LLDR+P LSGGQ+QRVA+GRAIVR P+ FL DEPLSNLDA+LR +MR E++ Sbjct: 119 AKLGLDPLLDRRPKALSGGQRQRVAMGRAIVRQPKAFLFDEPLSNLDARLREQMRAEIKK 178 Query: 180 LQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPM 239 L L T++YVTH+Q EAMT+ADRI M+ G +QQV SP + Y P NLFVA FIG P Sbjct: 179 LHKDLGATSIYVTHDQIEAMTLADRIVAMNGGVVQQVGSPLDLYDRPANLFVAGFIGSPG 238 Query: 240 INLVRGTRSESTF----VGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPDDAA 295 +N G + + PL D V + LG+RPE + +A P+ Sbjct: 239 MNFFEGAYHAGDAPRFEMSDEIGIPL--DAAAPVSNNSKVTLGIRPEHVVLAGHGPE--- 293 Query: 296 LDDHDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPPDK 355 L V +VEP G +LHLS A + T +T + V P Sbjct: 294 ----TLLAGVDLVEPTGFGIILHLS-----LGRAAFKVFTNDRSFLTASGTIPVHFPAHH 344 Query: 356 IHLFDAE 362 +H FDAE Sbjct: 345 LHFFDAE 351 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: 340 Number of extensions: 13 Number of successful extensions: 4 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: 355 Length adjustment: 30 Effective length of query: 353 Effective length of database: 325 Effective search space: 114725 Effective search space used: 114725 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: 49 (23.5 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