Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF4209 Psest_4282 spermidine/putrescine ABC transporter ATP-binding subunit
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__psRCH2:GFF4209 Length = 383 Score = 223 bits (569), Expect = 5e-63 Identities = 135/342 (39%), Positives = 196/342 (57%), Gaps = 19/342 (5%) Query: 4 LTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEG 63 L +D VTK + + VAV+++SL I GE L+G SG GKST LRM+AG E TEG Sbjct: 23 LKIDRVTKKFDET-----VAVDDVSLSIHQGEIFALLGGSGSGKSTLLRMLAGFERPTEG 77 Query: 64 ELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEET 123 + L+ + + + +R I M+FQSYAL+PH +V N++FGL++ GLP EI +RV+E Sbjct: 78 RIFLDGQDITDMPPYERPINMMFQSYALFPHMTVEQNIAFGLKQD-GLPKAEIEERVKEM 136 Query: 124 TDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQ 183 ++ ++ RKP QLSGGQ+QRVAL R++ + P++ L+DEP+ LD KLR++M+ EL Sbjct: 137 LGLVQMTQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLELV 196 Query: 184 RLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEP 243 ++ +GVT V VTHDQ EAMTM +R+A++ G + QVG+P+D Y P + V FIG Sbjct: 197 QIIERVGVTCVMVTHDQEEAMTMAERIAIMHLGWIAQVGSPMDIYETPASRLVCEFIG-- 254 Query: 244 SMNLFDGSLSGD-----TFRGDGFDYPL-SGATRDQLGGASGLTLGIRPEDVTVGE---- 293 ++NLFDG L D G + P+ G +T IRPE + +G Sbjct: 255 NVNLFDGELIEDMGDHAVIASPGLENPIYVGHGISTRAEDKQITYAIRPEKLLIGTELPE 314 Query: 294 -RRSGQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATT 334 R G V + G + +++ G F A T Sbjct: 315 LERPGYNWAKGVVHDIAYLGGHSVYYIKLPSGGVLQAFMANT 356 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: 375 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: 383 Length adjustment: 30 Effective length of query: 353 Effective length of database: 353 Effective search space: 124609 Effective search space used: 124609 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