Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate PP_0411 PP_0411 Polyamine ABC transporter, ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Putida:PP_0411 Length = 374 Score = 230 bits (586), Expect = 6e-65 Identities = 121/233 (51%), Positives = 159/233 (68%), Gaps = 3/233 (1%) Query: 14 GDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIGGDHMNYRVPQ 73 G+++ V DL+LDI EFL L+GPSG GK+T+L MLAG ETPT+G+I +GG +N P Sbjct: 26 GESLIVKDLNLDIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEIQLGGRSINNVPPH 85 Query: 74 NRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLGIADLLDRKPD 133 RDI MVFQ+YAL+PHMTV +N+ F L + + ERV V + + R P Sbjct: 86 KRDIGMVFQNYALFPHMTVAENLAFPLTVRN-LSKTDISERVKRVLNMVQLDAFAKRYPG 144 Query: 134 ELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQLAVTTVYVTH 193 +LSGGQQQRVAL RA+V +P++ LMDEPL LD +LR M+ E++++ +L VT VYVTH Sbjct: 145 QLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHIHQRLGVTVVYVTH 204 Query: 194 NQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMINLVRGT 246 +Q EA+TM+DR+AV GE+QQ+A P Y EP N FVA FIGE N + GT Sbjct: 205 DQGEALTMSDRVAVFHQGEIQQIADPRTLYEEPCNTFVANFIGEN--NRISGT 255 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: 348 Number of extensions: 9 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: 374 Length adjustment: 30 Effective length of query: 353 Effective length of database: 344 Effective search space: 121432 Effective search space used: 121432 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 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