Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate HSERO_RS01355 HSERO_RS01355 sugar ABC transporter ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__HerbieS:HSERO_RS01355 Length = 381 Score = 286 bits (733), Expect = 5e-82 Identities = 174/394 (44%), Positives = 230/394 (58%), Gaps = 28/394 (7%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA +TL K Y D + + LDI + EF V +GPSGCGKST LR +AGLE + Sbjct: 1 MASITLRAAQKAYGDAPP----VIRNVDLDIGEHEFCVFLGPSGCGKSTLLRSIAGLEDL 56 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 T G+L + + +N V + R +AMVFQSYAL+PH +V NMSFGL + LP EI Q+V Sbjct: 57 TSGDLFIGGKRVNDVPSAQRSVAMVFQSYALFPHMTVYENMSFGLTLAK-LPKAEIEQKV 115 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 E +L + +LL RKP +LSGGQ+QRVA+GRAIVR P VFL DEPLSNLDA LR++ R Sbjct: 116 REAARILQLEELLQRKPKELSGGQRQRVAIGRAIVRRPGVFLFDEPLSNLDATLRSQTRI 175 Query: 181 ELQRLQGEL-GVTTVYVTHDQTEAMTMGDRVAVLDD-------GELQQVGTPLDCYHRPN 232 E+ RL + + VYVTHDQ EAMT+ DR+ +L G + QVGTP++ YH P Sbjct: 176 EIARLHRQFEQASVVYVTHDQVEAMTLADRIVLLHAGADTQRFGSIAQVGTPMELYHHPR 235 Query: 233 NLFVAGFIGEPSMNLFDGSLSGDTFRGDGFDYPLSGATRDQLGGASG-------LTLGIR 285 N FVAGFIG P MN ++G + +G LSG+ L A G +T+G+R Sbjct: 236 NRFVAGFIGSPRMNFLPAQVAG--VQENGILVRLSGSEETLLVAAQGALQPGQMVTVGVR 293 Query: 286 PEDVTVGERRSGQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDR 345 PE + +G + GQ EVV+VE G + VHL D G A G +R+ G+R Sbjct: 294 PEHMEIGSQ--GQYGIHREVVLVERLGEQTYVHL---DEPAGQPLVAKAAGDARITRGER 348 Query: 346 TTVSFPEDAIHLFDGETGDALKNRELPSNRAIDA 379 V+ +LFD + G AL ++ A+ A Sbjct: 349 VRVAIAPACAYLFD-QDGLALTRTQVQGGLAVAA 381 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: 21 Number of successful extensions: 7 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: 381 Length adjustment: 30 Effective length of query: 353 Effective length of database: 351 Effective search space: 123903 Effective search space used: 123903 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