Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF960 HP15_939 spermidine/putrescine ABC transporter ATPase subunit
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__Marino:GFF960 Length = 372 Score = 204 bits (518), Expect = 4e-57 Identities = 126/341 (36%), Positives = 189/341 (55%), Gaps = 18/341 (5%) Query: 22 VAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNGVSAQDRD 81 +AV+ ++LDI GE L+G SG GKST LRM+AG ET G + L+ + + + R Sbjct: 28 LAVDNVNLDIHKGEIFALLGGSGSGKSTLLRMLAGFETPNAGSIMLDGQDVTALPPFLRP 87 Query: 82 IAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETTDMLGISDLLDRKPGQLS 141 M+FQSYAL+PH +V N++ GL++ LP EIR RV ++ + RKP QLS Sbjct: 88 TNMMFQSYALFPHMTVEQNIAMGLKQDK-LPKSEIRDRVAAMLKLVKMEPYARRKPQQLS 146 Query: 142 GGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVYVTHDQT 201 GGQQQRVAL R++ + P++ L+DEP+ LD KLR EM+ EL + +G T + VTHDQ Sbjct: 147 GGQQQRVALARSLAKRPKLLLLDEPMGALDKKLRTEMQLELVEILENVGATCLMVTHDQE 206 Query: 202 EAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNLFDGSLSGD-----T 256 EAMTM R+A++ G + Q+G+P+D Y PN+ A FIG S+N+F+ + D T Sbjct: 207 EAMTMASRIAIMAQGRIAQIGSPIDIYESPNSRMTAEFIG--SVNIFEAHIREDEADSVT 264 Query: 257 FRGDGFDYPL---SGATRDQLGGASGLTLGIRPEDV-TVGERRSGQRTFDAEVV-VVEPQ 311 D D P+ G T ++ + +RPE + ++ G+ + V + Sbjct: 265 LTSDLLDAPVFIDRGVTTP--AESTATLVALRPEKIYLTPDKPDGENNWSCGTVDNIAYL 322 Query: 312 GNENAVHLRFVDGD--EGTQFTATTTGQSRVEAGDRTTVSF 350 G+ + +++ G + T G+ R GDR VS+ Sbjct: 323 GDITSYYVKLASGKRVQATMANVERRGE-RPTWGDRVFVSW 362 Lambda K H 0.316 0.136 0.384 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: 368 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: 372 Length adjustment: 30 Effective length of query: 353 Effective length of database: 342 Effective search space: 120726 Effective search space used: 120726 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: 42 (22.0 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