Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate BPHYT_RS05040 BPHYT_RS05040 sugar ABC transporter ATPase
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__BFirm:BPHYT_RS05040 Length = 371 Score = 298 bits (763), Expect = 2e-85 Identities = 174/374 (46%), Positives = 233/374 (62%), Gaps = 26/374 (6%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA L++ DV K Y + + ++ +++DI+DG+FL+LVG SGCGKST L M+AGLETV Sbjct: 1 MASLSIRDVYKTYPN----GVPVLKGVNIDIEDGQFLILVGGSGCGKSTLLNMIAGLETV 56 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 T+GE++++ + +N +S +DRDIAMVFQSYALYP +VR N+SFGL +P +E Q V Sbjct: 57 TKGEIQIDGKTVNNLSPKDRDIAMVFQSYALYPSMTVRENISFGLNIRK-VPKNEQTQIV 115 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 + ++ L I+ LLDRKPGQLSGGQ+QRVA+GRA+ RDP +FL DEPLSNLDAKLR EMR+ Sbjct: 116 DRVSNTLQITHLLDRKPGQLSGGQRQRVAMGRALARDPVMFLFDEPLSNLDAKLRIEMRS 175 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 E++ L LG T VYVTHDQ EAMT+GDR+AV+ DG +QQ G P + Y P+NLFVAGFI Sbjct: 176 EIKLLHQRLGTTIVYVTHDQIEAMTLGDRIAVMKDGIVQQFGAPQEIYDSPSNLFVAGFI 235 Query: 241 GEPSMNLFDGSL----SGDTFRGD------GFDYPLSGA-TRDQLGGASGLTLGIRPEDV 289 G P MN G L +G D + P A R +G + LG+RPE + Sbjct: 236 GAPPMNFIQGKLVEQGAGVALELDTGVARTALNLPFDSAKVRSHVG--REVILGLRPERI 293 Query: 290 TVGERRSGQ----RTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDR 345 T G + + +V V+EP G + V + G + + S + Sbjct: 294 TDARGAHGDNAKLQPIEVKVDVIEPTGPDTLVFAQV----NGKRIVSRVHPASNPQPLAN 349 Query: 346 TTVSFPEDAIHLFD 359 TT+ F LFD Sbjct: 350 TTLLFDTSKAVLFD 363 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: 436 Number of extensions: 28 Number of successful extensions: 2 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: 371 Length adjustment: 30 Effective length of query: 353 Effective length of database: 341 Effective search space: 120373 Effective search space used: 120373 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: 50 (23.9 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