Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_024851725.1 N745_RS0108650 ABC transporter ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >NCBI__GCF_000526715.1:WP_024851725.1 Length = 282 Score = 143 bits (360), Expect = 7e-39 Identities = 82/208 (39%), Positives = 126/208 (60%), Gaps = 10/208 (4%) Query: 7 TDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIGGDH 66 T +TK+ G ++ + L + + EF+ LVG SGCGKST LR++ GLE T G + + + Sbjct: 13 TFITKK-GAVEVLESIDLTVKENEFVALVGASGCGKSTLLRIIGGLEKLTKGQVLVDEEI 71 Query: 67 MNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEE-EGYTSAERD-----ERVVEVAE 120 +N +D AMVFQDY+LYP +TV++NI+F + G + D +R + + Sbjct: 72 VN---KPGKDRAMVFQDYSLYPWLTVKENIQFSRNLKINGQGNGLGDIGSMVDRSYALLD 128 Query: 121 TLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180 +G+ + D P++LSGG +QRVA+ RA++ P+V LMDEP LDA+ R M + +L Sbjct: 129 LMGLEKVQDSHPNQLSGGMRQRVAIARALMSKPDVLLMDEPFGALDAQTREVMHDLILHL 188 Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVM 208 + T V+VTH+ EA+ +ADR+ VM Sbjct: 189 FEIEKSTIVFVTHDVEEAIYLADRVVVM 216 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: 249 Number of extensions: 10 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: 282 Length adjustment: 28 Effective length of query: 355 Effective length of database: 254 Effective search space: 90170 Effective search space used: 90170 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 Apr 09 2024. 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