Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF2690 PGA1_c27320 putative sugar ABC transporter, ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__Phaeo:GFF2690 Length = 349 Score = 290 bits (741), Expect = 6e-83 Identities = 168/367 (45%), Positives = 229/367 (62%), Gaps = 21/367 (5%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA++ L +++K + G V V+ L I D EFLVL+GPSGCGK+TT+RM+AGLE+ Sbjct: 1 MAQIELRNISKRW-----GSFVGVDNFDLTIADKEFLVLLGPSGCGKTTTMRMIAGLESA 55 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 +EG++ ++ +N + +DRD+AMVFQSYALYP+ +V N+ F L+ G+ ++V Sbjct: 56 SEGDILVDGNRVNELEPKDRDVAMVFQSYALYPNMNVYENIRFPLKVR-GVDAKTHDEKV 114 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 + M+ + + L RKP +LSGGQ+QRVAL RAIVR+P VFLMDEPLSNLDAKLR R Sbjct: 115 RRASAMVELDEFLHRKPAELSGGQRQRVALARAIVREPNVFLMDEPLSNLDAKLRVSTRA 174 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 +++ L EL VTT+YVTHDQ EAMT+ DRV V++ G +QQVG+P + Y RP N FVA FI Sbjct: 175 QIKNLSHELAVTTIYVTHDQIEAMTLADRVVVMNKGVVQQVGSPTEIYDRPANAFVASFI 234 Query: 241 GEPSMNLFDGSLSGDTFRGDGFDYPLSGATRDQLGGASG-LTLGIRPEDVTVGERRSGQR 299 G P+MNL +G LSG F D ++G L G G +TLG R ED +V + GQ Sbjct: 235 GSPAMNLMEGGLSGGRFTAQHTD--IAG-----LSGQDGPVTLGFRAEDASVVD-SGGQ- 285 Query: 300 TFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHLFD 359 +A + +E G+ V +R G + R E D ++ P D HLFD Sbjct: 286 -INAPIYTMELLGDATMVTVRI----GGVLVSVKADKTFRAEIDDMVSIHVPTDHCHLFD 340 Query: 360 GETGDAL 366 +TG L Sbjct: 341 TQTGARL 347 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: 423 Number of extensions: 22 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