Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF1645 PGA1_c16680 sugar ABC transporter, ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__Phaeo:GFF1645 Length = 355 Score = 298 bits (764), Expect = 1e-85 Identities = 177/369 (47%), Positives = 229/369 (62%), Gaps = 19/369 (5%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MAR+ L DV K Y G + + +I+LDI DGEF+VLVGPSGCGKST LRM+AGLE + Sbjct: 1 MARIELRDVAKRY-----GAVEVLRDINLDIQDGEFIVLVGPSGCGKSTLLRMIAGLEPI 55 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 T G+ ++ + +N V +DRDIAMVFQSYALYPH V NM F +E P +E R RV Sbjct: 56 TSGDFEIDGQRMNDVRPRDRDIAMVFQSYALYPHMDVARNMGFSMEIRKD-PAEERRSRV 114 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 + LG+S L+DR P LSGGQ+QRVA+GRAI+RDP FL DEPLSNLDA LR EMR Sbjct: 115 ARAAETLGLSSLVDRLPKALSGGQRQRVAMGRAIIRDPRAFLFDEPLSNLDAALRVEMRL 174 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 E+ RL +LG T +YVTHDQ EA+T+ DR+ VL+ G++QQVG+PL+ Y RP N FVA FI Sbjct: 175 EIARLHKQLGATMIYVTHDQVEALTLADRIVVLNGGDIQQVGSPLELYERPANKFVAQFI 234 Query: 241 GEPSMNLF--DGSLSGDTFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQ 298 G P+MN+ G+ SG +G L A+ + LGIRPE + V E G Sbjct: 235 GSPTMNILPVSGAASG-VMATNGMMLTLD----HMHDTAAAVELGIRPEHLDVVEPGEGH 289 Query: 299 RTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHLF 358 A+ VVE G++ ++ + VDG G V +G+R + H+F Sbjct: 290 LIAVAD--VVERLGSDTNIYAK-VDG--LGPLMVRKHGNVPVRSGERLGLRVQAQNAHIF 344 Query: 359 DGETGDALK 367 D + G AL+ Sbjct: 345 D-DRGIALR 352 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: 408 Number of extensions: 18 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: 355 Length adjustment: 30 Effective length of query: 353 Effective length of database: 325 Effective search space: 114725 Effective search space used: 114725 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