Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_043462293.1 H537_RS48490 ABC transporter ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >NCBI__GCF_000430725.1:WP_043462293.1 Length = 356 Score = 293 bits (750), Expect = 5e-84 Identities = 172/365 (47%), Positives = 221/365 (60%), Gaps = 17/365 (4%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 M L++ V K Y G++ ++ I +DI+ GEFL+LVGPSGCGKST L M+AGL+T Sbjct: 1 MGALSIRQVEKTYA----GNVRILKGIDIDIEAGEFLILVGPSGCGKSTLLSMIAGLDTP 56 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 T G + + +R + + ++DRDIAMVFQSYALYP+ +V N++FGLE +P E V Sbjct: 57 TAGSIHIGERDVTHLPSKDRDIAMVFQSYALYPNMTVAQNVAFGLEIRK-VPRAEREAAV 115 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 + ML I LLDRKPGQLSGGQ+QRVA+GRA+ R+P++FL DEPLSNLDAKLR EMR Sbjct: 116 DRVAKMLQIGHLLDRKPGQLSGGQRQRVAMGRALARNPKLFLFDEPLSNLDAKLRVEMRA 175 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 E++ L TTVYVTHDQ EAMT+GDR+AV+ DG +QQ GTP D Y RP N FVA FI Sbjct: 176 EIKLLHQRTRTTTVYVTHDQVEAMTLGDRIAVMKDGVVQQFGTPEDIYTRPVNRFVAEFI 235 Query: 241 GEPSMNLFDGSLSGDTFRGDGFDYPLSGATRDQL---GGASGLTLGIRPEDVTVGERRSG 297 G P MN+ S G G + P + A R L GA L G+RPE + + SG Sbjct: 236 GSPVMNIVAASRGGIGATAGGLELPTTDAQRAALRAGAGAGELLYGLRPEHLALD--HSG 293 Query: 298 QRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHL 357 + ++EP G + VD G Q TA G G+ + + HL Sbjct: 294 ---VPGRLAIIEPTGPDT---YATVDTPLG-QLTARVPGVLHAGVGENVHLRWQPQHAHL 346 Query: 358 FDGET 362 FD T Sbjct: 347 FDART 351 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: 412 Number of extensions: 26 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 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