Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF1168 PS417_05935 polyamine ABC transporter ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__WCS417:GFF1168 Length = 344 Score = 227 bits (578), Expect = 4e-64 Identities = 134/345 (38%), Positives = 196/345 (56%), Gaps = 33/345 (9%) Query: 19 GDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNGVSAQ 78 G++ AV+ +S+DI DGEF ++GPSG GK+T LR++AG E + G +R+ G+ Sbjct: 15 GEVKAVDRVSIDIQDGEFFSMLGPSGSGKTTCLRLIAGFEQPSAGSIRIHGEEAAGLPPY 74 Query: 79 DRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETTDMLGISDLLDRKPG 138 RD+ VFQ YAL+PH +VR N+++GL+ G+ E R EE M+ + DRKP Sbjct: 75 QRDVNTVFQDYALFPHMNVRDNVAYGLKVK-GVGKTERMNRAEEALGMVALGGYGDRKPV 133 Query: 139 QLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVYVTH 198 QLSGGQ+QRVAL RA+V P V L+DEPL LD KLR +M++EL++LQ +LG+T ++VTH Sbjct: 134 QLSGGQRQRVALARALVNRPRVLLLDEPLGALDLKLREQMQSELKKLQRQLGITFIFVTH 193 Query: 199 DQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNLFDGSLSGDTFR 258 DQTEA++M DRVAV + G ++QV TP + Y +P FVA F+G + N+ G L+ Sbjct: 194 DQTEALSMSDRVAVFNKGRIEQVDTPRNLYMKPATSFVAEFVG--TSNVIRGELA----- 246 Query: 259 GDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQRTFDAEVVV--VEPQGNENA 316 +LGG + IRPE V E G + ++ ++ QG+ Sbjct: 247 -------------QRLGG-TAQPFSIRPEHVRFAEGPLGTGEVEISGLLHDIQYQGSATR 292 Query: 317 VHLRFVDGD------EGTQFTATTTGQSRVEAGDRTTVSFPEDAI 355 L+ +G Q+ TT G + G T + +A+ Sbjct: 293 YELKLENGQALNISRANNQWLDTTAGH---QVGQTLTARWAREAM 334 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: 366 Number of extensions: 22 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: 344 Length adjustment: 29 Effective length of query: 354 Effective length of database: 315 Effective search space: 111510 Effective search space used: 111510 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