Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate PP_1484 PP_1484 predicted polyamine ABC transporter, ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__Putida:PP_1484 Length = 343 Score = 220 bits (561), Expect = 4e-62 Identities = 133/350 (38%), Positives = 199/350 (56%), Gaps = 27/350 (7%) Query: 19 GDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNGVSAQ 78 G++ AV+++S+DI DGEF ++GPSG GK+T LR++AG E + G +R++ G+ Sbjct: 15 GEVKAVDQVSIDIIDGEFFSMLGPSGSGKTTCLRLIAGFEQPSSGSIRIQGVEAAGLPPY 74 Query: 79 DRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETTDMLGISDLLDRKPG 138 RD+ VFQ YAL+PH +V N+++GL+ G+ E R EE M+ ++ RKP Sbjct: 75 QRDVNTVFQDYALFPHMNVLENIAYGLKVK-GVGKAERHSRAEEALAMVALAGYGARKPA 133 Query: 139 QLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVYVTH 198 QLSGGQ+QRVAL RA+V P V L+DEPL LD KLR +M+ EL++LQ +LG+T ++VTH Sbjct: 134 QLSGGQRQRVALARALVNRPRVLLLDEPLGALDLKLREQMQGELKKLQRQLGITFIFVTH 193 Query: 199 DQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNLFDGSLSGDTFR 258 DQTEA++M DRVAV + G ++QV TP + Y +P+ FVA F+G + N+ G L+ Sbjct: 194 DQTEALSMSDRVAVFNRGRIEQVDTPRNLYMKPSTTFVAEFVG--TSNVVRGELA----- 246 Query: 259 GDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQRTFDAEVVV--VEPQGNENA 316 Q+ G S IRPE + +G+ V+ V+ QG+ Sbjct: 247 -------------MQING-SPAPFSIRPELIRLGDPVVTSHEVQVSGVLHDVQYQGSATR 292 Query: 317 VHLRFVDGDEGTQFTATTTGQSRVEA---GDRTTVSFPEDAIHLFDGETG 363 L+ +G A Q +++A G R +P +A+ + G Sbjct: 293 YELQLDNGQLLAVSQANDRWQKQMQAWQLGQRLQAHWPREAMTVLQETEG 342 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: 363 Number of extensions: 24 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: 343 Length adjustment: 29 Effective length of query: 354 Effective length of database: 314 Effective search space: 111156 Effective search space used: 111156 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: 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