Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_085543660.1 B9Y55_RS01865 ABC transporter ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >NCBI__GCF_900177735.1:WP_085543660.1 Length = 358 Score = 233 bits (595), Expect = 5e-66 Identities = 137/333 (41%), Positives = 195/333 (58%), Gaps = 11/333 (3%) Query: 23 AVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNGVSAQDRDI 82 AV+E+ LD+ GE + +GPSGCGK+TTLRM+AG ET T G + ++ + + V R I Sbjct: 23 AVKELDLDVKGGELVTFLGPSGCGKTTTLRMVAGFETPTSGRILIDGQDVTDVMVNKRHI 82 Query: 83 AMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETTDMLGISDLLDRKPGQLSG 142 VFQ+YAL+PH +V N+++GL D I+ +V + +M+G+S + R P QLSG Sbjct: 83 GFVFQNYALFPHMTVGDNVAYGLRMRNESAKD-IKTKVVQGLEMVGLSQVEKRYPNQLSG 141 Query: 143 GQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVYVTHDQTE 202 G+QQRVAL R +V P+V LMDEPLSNLDAKLR MRTE++R+Q +L +T +YVTHDQ E Sbjct: 142 GEQQRVALARVLVMRPKVLLMDEPLSNLDAKLRIHMRTEIRRIQKQLDITCLYVTHDQKE 201 Query: 203 AMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNLFDGS---LSGDTFRG 259 A+TM DR+ V++ G+++Q+GTP Y P + FVA FIG+ N+ +G+ L G T R Sbjct: 202 ALTMADRIMVMNKGQVEQIGTPFQIYTAPESTFVADFIGQ--ANILEGTLDDLDGLTSRI 259 Query: 260 DGFDYPLSGATRDQLGGASG--LTLGIRPEDVTVGERRSGQRTFDAEVVVVEPQGNENAV 317 LS + G ++L +RPE +++ + G V V G+ Sbjct: 260 STGGSNLSARLLEGKSYRKGEKVSLVLRPETLSLSQ---GGGLLGGTVTQVVFSGDRMEY 316 Query: 318 HLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSF 350 LR DG G + GD +SF Sbjct: 317 TLRLGDGQSLLAMENFYPGIKVWQEGDSVDLSF 349 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: 407 Number of extensions: 19 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: 358 Length adjustment: 30 Effective length of query: 353 Effective length of database: 328 Effective search space: 115784 Effective search space used: 115784 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 24 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