Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate N515DRAFT_4212 N515DRAFT_4212 multiple sugar transport system ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__Dyella79:N515DRAFT_4212 Length = 364 Score = 294 bits (753), Expect = 2e-84 Identities = 171/372 (45%), Positives = 228/372 (61%), Gaps = 26/372 (6%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA++ LD + KVY + V V E S +I DGE LVLVGPSGCGK+T LRM+AGLE++ Sbjct: 1 MAKVRLDKLRKVYPNGH----VGVAEASFEIADGELLVLVGPSGCGKTTLLRMIAGLESI 56 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 + G L + +RV+N ++ +DRDIAMVFQ+YALYPH +V N+ FGL+ G P EI +RV Sbjct: 57 SGGTLSIGERVVNDIAPKDRDIAMVFQNYALYPHMTVAENLGFGLK-LRGQPKAEIERRV 115 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 E ML + LD +P LSGGQ+QRVALGRA+VRDP+VFL+DEPLSNLDAKLR MR Sbjct: 116 AEAARMLELEQRLDSRPAALSGGQRQRVALGRALVRDPKVFLLDEPLSNLDAKLRLSMRV 175 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 E+ R+ L T VYVTHDQ EAMT+G R+ VL+ G +QQ+ TP++ Y P NLFVAGF+ Sbjct: 176 EIARIHQRLKATMVYVTHDQIEAMTLGQRIVVLNGGVIQQIDTPMNLYDTPANLFVAGFL 235 Query: 241 GEPSMNLFDGSL-----------SGDTFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDV 289 G P+MNL G L G+ G+ A RD+ + +G+RPED+ Sbjct: 236 GSPAMNLLRGILYRDGGWKLAMPQGELVLGELPQGAALEAWRDR-----DIVVGLRPEDL 290 Query: 290 TVGERRSGQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVS 349 + +G A++ VVEP GNE ++LR + + + G Sbjct: 291 LLCADAAG-AALAAQLEVVEPVGNEVFLNLRHGE----LALVSRMPPRELPAPGSTLHFG 345 Query: 350 FPEDAIHLFDGE 361 F + +H FD + Sbjct: 346 FAPERLHFFDAK 357 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: 413 Number of extensions: 22 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: 364 Length adjustment: 30 Effective length of query: 353 Effective length of database: 334 Effective search space: 117902 Effective search space used: 117902 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 Sep 17 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