Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate CCNA_01506 CCNA_01506 cystine transport ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Caulo:CCNA_01506 Length = 246 Score = 135 bits (341), Expect = 9e-37 Identities = 88/232 (37%), Positives = 120/232 (51%), Gaps = 12/232 (5%) Query: 1 MGQIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDI 60 M I L K FGDT + + L + E + ++GPSG GKST LR LAGLE GD+ Sbjct: 1 MSAIDAKSLKKSFGDTPVLAGVDLAVVPGEVVAIIGPSGSGKSTLLRCLAGLEPLNDGDL 60 Query: 61 YIGGDHMNYRVPQ----NRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVV 116 I G + P N + VFQ + L+PH T +N+ G A+ + + Sbjct: 61 TIAGVAAGGKTPLAKALNGRVGFVFQSFNLFPHRTALENVIEGPIVVRREDPAKARAKGL 120 Query: 117 EVAETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTE 176 + E +G+AD +D P LSGGQQQR A+ RA+ DPEV L DEP S LD +L E+ Sbjct: 121 ALLEKVGLADRVDAYPSALSGGQQQRCAIARALAMDPEVILFDEPTSALDPELVGEVLAV 180 Query: 177 LQNLQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGEL-------QQVASPFE 221 +++L + T V VTH A +A+R MD G + Q +ASP E Sbjct: 181 IRDLAAEKR-TMVIVTHQMDFARDVAERTIFMDGGVIVEQGPSRQLLASPRE 231 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: 195 Number of extensions: 6 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: 246 Length adjustment: 27 Effective length of query: 356 Effective length of database: 219 Effective search space: 77964 Effective search space used: 77964 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