Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >NCBI__GCF_002019605.1:WP_078429421.1 Length = 351 Score = 207 bits (528), Expect = 3e-58 Identities = 110/259 (42%), Positives = 164/259 (63%), Gaps = 12/259 (4%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 M+ + D+VTK Y AV++++L+I +GE + L+GPSGCGK+TTLRM+AG E Sbjct: 1 MSFIQFDNVTKYYNRAA---TPAVDQLNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQP 57 Query: 61 TEGELRLEDRVL----NGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEI 116 T G++R+ D V+ + + R I MVFQ YAL+PH ++ N++FGL + + Sbjct: 58 TTGKIRIGDEVVYDDRRALPPEKRGIGMVFQDYALFPHLTIEKNVTFGLNR---WKNRDK 114 Query: 117 RQRVEETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRA 176 ++R +E +++G+ + R P +LSGGQQQRVAL RA+ P+V LMDEP SNLDA LR Sbjct: 115 KKRAQEVLELVGLGEFGHRLPSELSGGQQQRVALARALAPRPKVILMDEPFSNLDAGLRE 174 Query: 177 EMRTELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFV 236 +MR ++ + + T + VTHDQ +A + DRV V+++G +QQ+ P + Y P N FV Sbjct: 175 KMRYDVTNILRKANATAIIVTHDQKDAFAVSDRVVVMNEGIIQQIAAPKEMYRCPANCFV 234 Query: 237 AGFIGEPSMNLFDGSLSGD 255 A F+G+ NL G+L D Sbjct: 235 AQFVGK--TNLISGTLCPD 251 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: 337 Number of extensions: 15 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: 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 Apr 09 2024. 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