Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_015448118.1 R2APBS1_RS12060 ABC transporter ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >NCBI__GCF_000230695.2:WP_015448118.1 Length = 255 Score = 139 bits (349), Expect = 1e-37 Identities = 84/233 (36%), Positives = 126/233 (54%), Gaps = 4/233 (1%) Query: 6 LTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIGGD 65 L KR+G A++ +SL L+G SG GKST LR+L GLE P G + + G Sbjct: 14 LVQAGKRYGRLQALEQVSLAFAAGTTTALIGSSGSGKSTVLRLLLGLEWPDHGHVEVDGR 73 Query: 66 HMNYR--VPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLG 123 + +P R + V QD L+PH+T N+ L G+ +R ++A Sbjct: 74 PLQRSDVLPLRRRVGYVIQDGGLFPHLTALGNLAL-LPRHLGWNRERIRQRAEQLAALTH 132 Query: 124 I-ADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQD 182 + +L+R P ELSGGQ+QRVAL RA++ DP+ L+DEPL LD +R E++ EL+ + D Sbjct: 133 LPTGVLERYPAELSGGQRQRVALMRALMADPDALLLDEPLGALDPVVRHELQDELKQIFD 192 Query: 183 QLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFI 235 QL T + VTH+ EA A+R+ ++ G + Q + + P + FV F+ Sbjct: 193 QLGKTVIVVTHDLAEAAWFAERLVLLRQGAVLQDGTFRDLRERPADAFVNRFV 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: 199 Number of extensions: 4 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: 255 Length adjustment: 27 Effective length of query: 356 Effective length of database: 228 Effective search space: 81168 Effective search space used: 81168 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 24 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