Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate SMc02474 SMc02474 ABC transporter ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__Smeli:SMc02474 Length = 356 Score = 313 bits (801), Expect = 6e-90 Identities = 174/371 (46%), Positives = 235/371 (63%), Gaps = 20/371 (5%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA + L D+ K Y + V +SL I +GEF+ LVGPSGCGKST LRM+AGLE + Sbjct: 1 MASVELRDIRKSYAA-----LEVVHGVSLSIAEGEFIALVGPSGCGKSTLLRMIAGLEEI 55 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 ++GE+ + +V+N ++ ++R+IAMVFQSYALYPH SV NM F L+ S GL EI ++V Sbjct: 56 SDGEVLIGGKVVNPLTPRERNIAMVFQSYALYPHMSVAENMGFNLKLS-GLSRPEIDKKV 114 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 E ML +++LLDRKP QLSGGQ+QR A+GRAIVRDP VFL DEPLSNLDAKLR +MRT Sbjct: 115 GEAARMLALTELLDRKPSQLSGGQRQRAAMGRAIVRDPAVFLFDEPLSNLDAKLRVQMRT 174 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 E++ L ++ T++YVTHDQ EAMT+ DR+ VL+ G ++QVGTPL+ Y P NLFVAGFI Sbjct: 175 EIKALHQKVATTSIYVTHDQIEAMTLADRIVVLNGGRIEQVGTPLELYRTPANLFVAGFI 234 Query: 241 GEPSMNLFDGSLSGDTFR-----GDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERR 295 G P+MN+ DG++ D GDG ++ + + G A + +G+RPE G Sbjct: 235 GSPAMNVLDGTVDADDGEPAVRLGDGSAIRIAPERKVRPGQA--VRIGLRPEHFVAGGEG 292 Query: 296 SGQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAI 355 + + ++VEP G + V F G Q TA G G + + Sbjct: 293 N---AIAGQTLLVEPTGAQTHVLFEFA----GEQITAVVDGDHPARHGSLFRAAMDRSQV 345 Query: 356 HLFDGETGDAL 366 ++FD +TG AL Sbjct: 346 YVFDRQTGAAL 356 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: 463 Number of extensions: 27 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: 356 Length adjustment: 30 Effective length of query: 353 Effective length of database: 326 Effective search space: 115078 Effective search space used: 115078 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