Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate CA265_RS15880 CA265_RS15880 sugar ABC transporter ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Pedo557:CA265_RS15880 Length = 330 Score = 141 bits (355), Expect = 3e-38 Identities = 76/243 (31%), Positives = 140/243 (57%), Gaps = 9/243 (3%) Query: 4 IQLTDLTKRFGDTVA--VDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIY 61 I + +LTK++ A + ++S +I + + ++G SG GKST L+ + GL G+I+ Sbjct: 6 ISVKNLTKQYQAEQAGGIKNVSFEIKQGDVVAIIGESGSGKSTLLKSIYGLLKTDEGEIF 65 Query: 62 IGGDHMN----YRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVE 117 + +P ++ + MV QD++L + V NI L + T AE+ ++ Sbjct: 66 FEDKRVKGPDEQLIPGHKQMKMVTQDFSLNIYAKVYDNIASQLSNTDLKTKAEK---TLQ 122 Query: 118 VAETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTEL 177 + E L I L ++K ELSGG+QQRVA+ +A+V D +V L+DEP S +DA L+ ++R ++ Sbjct: 123 IMEHLRILPLQNKKIIELSGGEQQRVAIAKAMVADTQVLLLDEPFSQVDALLKNQLRADI 182 Query: 178 QNLQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGE 237 + + + VT + V+H+ + + +AD++ ++ +GEL Q P E Y P +++ A+ +G Sbjct: 183 KRVASETGVTVILVSHDPADGLFLADQLLILKNGELLQTGKPSEIYQHPKHIYTAQILGN 242 Query: 238 PMI 240 ++ Sbjct: 243 AVV 245 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: 222 Number of extensions: 10 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: 383 Length of database: 330 Length adjustment: 29 Effective length of query: 354 Effective length of database: 301 Effective search space: 106554 Effective search space used: 106554 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