Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate BPHYT_RS05040 BPHYT_RS05040 sugar ABC transporter ATPase
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__BFirm:BPHYT_RS05040 Length = 371 Score = 273 bits (698), Expect = 6e-78 Identities = 159/328 (48%), Positives = 209/328 (63%), Gaps = 14/328 (4%) Query: 1 MGQIQLTDLTKRFGDTVAV-DDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGD 59 M + + D+ K + + V V +++DI+D +FL+LVG SGCGKST L M+AGLET T G+ Sbjct: 1 MASLSIRDVYKTYPNGVPVLKGVNIDIEDGQFLILVGGSGCGKSTLLNMIAGLETVTKGE 60 Query: 60 IYIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVA 119 I I G +N P++RDIAMVFQ YALYP MTVR+NI FGL + E+ + V V+ Sbjct: 61 IQIDGKTVNNLSPKDRDIAMVFQSYALYPSMTVRENISFGLNIRK-VPKNEQTQIVDRVS 119 Query: 120 ETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQN 179 TL I LLDRKP +LSGGQ+QRVA+GRA+ RDP +FL DEPLSNLDAKLR EMR+E++ Sbjct: 120 NTLQITHLLDRKPGQLSGGQRQRVAMGRALARDPVMFLFDEPLSNLDAKLRIEMRSEIKL 179 Query: 180 LQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPM 239 L +L T VYVTH+Q EAMT+ DRIAVM DG +QQ +P E Y P+NLFVA FIG P Sbjct: 180 LHQRLGTTIVYVTHDQIEAMTLGDRIAVMKDGIVQQFGAPQEIYDSPSNLFVAGFIGAPP 239 Query: 240 INLVRGTRSE----------STFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADA 289 +N ++G E + + P D + S R + +LG+RPE I A Sbjct: 240 MNFIQGKLVEQGAGVALELDTGVARTALNLPFDSAKVRSHVGR-EVILGLRPERITDARG 298 Query: 290 APDDAALDDHDLQMDVTVVEPHGDQNVL 317 A D A +++ V V+EP G ++ Sbjct: 299 AHGDNA-KLQPIEVKVDVIEPTGPDTLV 325 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: 373 Number of extensions: 11 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: 371 Length adjustment: 30 Effective length of query: 353 Effective length of database: 341 Effective search space: 120373 Effective search space used: 120373 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: 50 (23.9 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