Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_085544626.1 B9Y55_RS06870 ABC transporter ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >NCBI__GCF_900177735.1:WP_085544626.1 Length = 363 Score = 221 bits (564), Expect = 2e-62 Identities = 108/223 (48%), Positives = 152/223 (68%), Gaps = 1/223 (0%) Query: 15 DTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIGGDHMNYRVPQN 74 + AV D I+ E + L+GPSGCGK+TTLRM+ G E PT G I+IG D + Y P Sbjct: 25 NVTAVKDSDFVIEPGELVTLLGPSGCGKTTTLRMIGGFEVPTRGRIFIGSDDVTYLPPNQ 84 Query: 75 RDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLGIADLLDRKPDE 134 RD AMVFQ Y L+PHM V N+ +GL+ + S + +++V E +G+ +L R P Sbjct: 85 RDTAMVFQSYGLFPHMNVFDNVAYGLKLRK-VPSQDIEKKVTEFLRMVGLEELAKRPPSR 143 Query: 135 LSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQLAVTTVYVTHN 194 LSGGQQQRVAL R+++ +P V L+DEPLSNLDA LR +MR E++ +Q L +T VYVTH+ Sbjct: 144 LSGGQQQRVALARSLIVEPGVLLLDEPLSNLDALLREQMRVEIRRIQKSLNITAVYVTHD 203 Query: 195 QTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGE 237 + EAM+++DR+ VMD GE+ Q+ +P + Y +P + FVA F+G+ Sbjct: 204 RVEAMSLSDRVIVMDRGEVVQIGTPSQIYCDPVSSFVAGFVGK 246 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: 335 Number of extensions: 14 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: 363 Length adjustment: 30 Effective length of query: 353 Effective length of database: 333 Effective search space: 117549 Effective search space used: 117549 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 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