Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate 208681 DVU3161 ABC transporter, ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >MicrobesOnline__882:208681 Length = 349 Score = 274 bits (700), Expect = 3e-78 Identities = 161/363 (44%), Positives = 223/363 (61%), Gaps = 20/363 (5%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 M+ + LD V++ + GD+ AV+++S +++ G+ LVL+GPSGCGKSTTLR++AGLE+V Sbjct: 1 MSTIVLDKVSRHW-----GDVRAVDDVSFEVEQGDMLVLLGPSGCGKSTTLRLIAGLESV 55 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 T G + + R + + R +AMVFQSYAL+PH +VR N+ FGL +P E ++R+ Sbjct: 56 TSGRILIGGRDVTNLPPAQRQLAMVFQSYALFPHLTVRDNILFGLVVRK-VPAAERQKRL 114 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 + ++LG+ LL+RKPG+LSGGQQQRVALGRA+V + V LMDEPLSNLDAKLR EMR Sbjct: 115 DRAVEILGLGKLLERKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRQEMRR 174 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 E++ LQ LG+T VYVTHDQTEAM+M DR+ ++ G + Q TP + Y RP F FI Sbjct: 175 EIRALQQTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPTEMYSRPATAFAGSFI 234 Query: 241 GEPSMNLFDGSLSGDTFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQRT 300 G P MNL L G+ DG S + R + LGIRPE + + + G R Sbjct: 235 GTPPMNLV--RLQGN---DDGIRVAGSRSGRVTCHAGADCMLGIRPEHIRIVD--DGWR- 286 Query: 301 FDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHLFDG 360 A V VE G+ + + R G E + + G + G + PE+ +H+FD Sbjct: 287 --AVVESVEYLGSNSVLSCRV--GSE--ELSVVVHGVTDTVVGAEIYLHCPEEHVHIFDA 340 Query: 361 ETG 363 TG Sbjct: 341 ATG 343 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: 370 Number of extensions: 20 Number of successful extensions: 3 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: 349 Length adjustment: 30 Effective length of query: 353 Effective length of database: 319 Effective search space: 112607 Effective search space used: 112607 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