Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_085545740.1 B9Y55_RS12845 ABC transporter ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >NCBI__GCF_900177735.1:WP_085545740.1 Length = 351 Score = 243 bits (619), Expect = 8e-69 Identities = 141/349 (40%), Positives = 201/349 (57%), Gaps = 14/349 (4%) Query: 19 GDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNGVSAQ 78 GD VE++S + G L L+GPSGCGK+T L +AG + G++ + R + + Q Sbjct: 13 GDHRVVEDLSFEAPSGTLLSLLGPSGCGKTTVLNGIAGFLPLISGKILFDHREIQDLKTQ 72 Query: 79 DRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETTDMLGISDLLDRKPG 138 R+I MVFQ+YALYPH + N++F L GL +IR++VEE +M I +L RKPG Sbjct: 73 SRNIGMVFQNYALYPHMTAFENIAFPLRVM-GLTKGDIRRKVEEMAEMTQIGSILHRKPG 131 Query: 139 QLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVYVTH 198 Q+SGGQQQRVA+ RA+V+ P++ L+DEPLSNLDA LR EMR E++R+Q E G TT++VTH Sbjct: 132 QISGGQQQRVAISRALVKKPDLLLLDEPLSNLDAGLRIEMREEIRRIQRETGTTTLFVTH 191 Query: 199 DQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNLFDGSLSGDTFR 258 DQ EA++M DR+ +LD G +QQ GTP + Y P NLF A F G P +N+ +G +GD R Sbjct: 192 DQEEALSMSDRIVLLDRGTIQQQGTPQELYRSPANLFTARFFGNPPVNVLEGEGTGDGLR 251 Query: 259 GDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQRTFDAEVVVVEPQGNENAVH 318 P+ + G A+ T +R ED+ + F V+ E G ++ V Sbjct: 252 LGPTVLPVP----VKFGQAT--TAVVRCEDLRICAEGG---HFQGSVLSSEILGRDSLVK 302 Query: 319 LRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHLFDGETGDALK 367 + + EG G+ + + LFD ETG +L+ Sbjct: 303 VSW----EGGVLRLIVPSDRSPSPGENLALEVNLRELQLFDLETGKSLR 347 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: 380 Number of extensions: 17 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: 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 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