Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >NCBI__GCF_900129305.1:WP_073037934.1 Length = 365 Score = 254 bits (648), Expect = 4e-72 Identities = 153/361 (42%), Positives = 211/361 (58%), Gaps = 22/361 (6%) Query: 3 RLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTE 62 ++ + DV K Y G + AV +S +++G+ LV++GPSGCGK+T LR++AGLE VT Sbjct: 2 QIEIRDVRKDY-----GRVQAVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTS 56 Query: 63 GELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEE 122 G + + + + R+I+MVFQSYAL+PH +VR N+ FGL+ +P DEI +R++ Sbjct: 57 GTIHIAGTDVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRK-VPADEIERRLKR 115 Query: 123 TTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTEL 182 D+LG+S LD KPG+LSGG QQRVALGRAI+ + V LMDEPLSNLDAKLR MR E+ Sbjct: 116 VVDLLGLSGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREI 175 Query: 183 QRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGE 242 LQ LG+T +YVTHDQ EAMTM DR+ ++ DG++ Q +P + Y RP N FVA FIG Sbjct: 176 CSLQRRLGITMIYVTHDQVEAMTMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGT 235 Query: 243 PSMNLFD-GSLSGDTFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQRTF 301 P MN+ G G G D+ GIRPE++ + E SGQ Sbjct: 236 PPMNIVPLCPTQGGAALEPGGRLLFPGMDPDR------YLFGIRPENLRLAE--SGQ--- 284 Query: 302 DAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHLFDGE 361 A V E G++ V G + T G+ + G +++ ++LFD Sbjct: 285 PAMVTGREYLGSDTFVSCEI----HGQEVIVRTRGRRNIREGTVVHLTWDPGDVNLFDAR 340 Query: 362 T 362 T Sbjct: 341 T 341 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: 402 Number of extensions: 26 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: 365 Length adjustment: 30 Effective length of query: 353 Effective length of database: 335 Effective search space: 118255 Effective search space used: 118255 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 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