Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF4127 HP15_4067 spermidine/putrescine ABC transporter ATPase subunit
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Marino:GFF4127 Length = 362 Score = 230 bits (587), Expect = 4e-65 Identities = 117/229 (51%), Positives = 153/229 (66%), Gaps = 1/229 (0%) Query: 9 LTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIGGDHMN 68 L +RFG AVD +SLD+ F ++GPSGCGK+T LR+LAG + P GDI+I G+ MN Sbjct: 10 LVRRFGSNAAVDHVSLDVPAGTFFSILGPSGCGKTTLLRLLAGFDKPDQGDIHIRGERMN 69 Query: 69 YRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLGIADLL 128 P R + MVFQ AL+P MTV NI +GL+ + ER +R+ V E +G+ DL Sbjct: 70 DVPPNRRPVNMVFQHLALFPTMTVGDNIAYGLKRRK-MPLVERRKRIARVLEQVGLPDLE 128 Query: 129 DRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQLAVTT 188 R P ELSGGQ+QRVAL R +V +P + L+DEPL LD KLR +M+ EL++LQ Q T Sbjct: 129 HRNPQELSGGQRQRVALARCLVLEPTLLLLDEPLGALDLKLREQMKVELKHLQKQFGTTF 188 Query: 189 VYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGE 237 VY+TH+Q+EAM M+D++AVM DG QVA P E Y EP FVA F+G+ Sbjct: 189 VYITHDQSEAMVMSDQVAVMRDGRFDQVAPPEELYREPATPFVAGFVGD 237 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: 339 Number of extensions: 16 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: 362 Length adjustment: 30 Effective length of query: 353 Effective length of database: 332 Effective search space: 117196 Effective search space used: 117196 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