Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate 3607842 Dshi_1250 ABC transporter related (RefSeq)
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__Dino:3607842 Length = 351 Score = 297 bits (760), Expect = 3e-85 Identities = 165/368 (44%), Positives = 225/368 (61%), Gaps = 19/368 (5%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 M+ +TL K Y G+ V + L I DGEF V VGPSGCGKST LRM+AGLE Sbjct: 1 MSGITLRGAVKRY-----GETQVVHGVDLSIADGEFCVFVGPSGCGKSTLLRMIAGLEET 55 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 +EG + + R + + +R +AMVFQ+YALYPH +V NM FGL+ + G+P EI+ +V Sbjct: 56 SEGSIHIGARDVTRLDPSERGVAMVFQTYALYPHMTVAENMGFGLKMN-GVPKAEIKAKV 114 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 +++L + D L RKP LSGGQ+QRVA+GRAIVR PEVFL DEPLSNLDA+LR EMR Sbjct: 115 AAASEILKLDDYLARKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRV 174 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 E+ RL E+G T +YVTHDQ EAMT+ D++ VL G ++QVG PL+ Y P+N+FVAGFI Sbjct: 175 EIARLHKEIGATMIYVTHDQVEAMTLADKIVVLRAGRVEQVGAPLELYRDPDNVFVAGFI 234 Query: 241 GEPSMNLFDGSLSGDTFRGDGF-DYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQR 299 G P+MN DG + D G P+ GA G + +T+G+RP+ + + G Sbjct: 235 GSPAMNFLDGRIENDAVHLAGLPPLPVPGAA----GRSGPVTVGVRPQHIALEPGGDGYL 290 Query: 300 TFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHLFD 359 V + E G + ++LR G +G++ T + + G +S D + LF+ Sbjct: 291 -----VELTESLGGVSYLYLR---GADGSRLTVEAGEEDPIAEGTPVGLSLAPDRVMLFE 342 Query: 360 GETGDALK 367 ETG L+ Sbjct: 343 AETGQRLR 350 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: 441 Number of extensions: 27 Number of successful extensions: 4 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: 351 Length adjustment: 30 Effective length of query: 353 Effective length of database: 321 Effective search space: 113313 Effective search space used: 113313 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