Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC
Query= uniprot:D4GP39 (383 letters) >NCBI__GCF_000759345.1:WP_043527041.1 Length = 354 Score = 296 bits (758), Expect = 6e-85 Identities = 162/363 (44%), Positives = 235/363 (64%), Gaps = 17/363 (4%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA + L + K Y G++ AV+ I L+I DGEF+VLVGPSGCGKST LRM+AGLET+ Sbjct: 1 MASIQLTGLKKTYA----GNVEAVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETI 56 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 T+G L+++DRV+N + +RDIAMVFQ+YALYPH +V GN+++GL+ + G+ +EI +RV Sbjct: 57 TDGTLKIDDRVVNDLEPAERDIAMVFQNYALYPHMTVFGNLAYGLK-NRGVKREEIERRV 115 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 + ML I L+RKP +LSGGQ+QRVA+GRA+VR+P FL DEPLSNLDAKLR +MR Sbjct: 116 HDAAAMLEIEPFLERKPRKLSGGQRQRVAMGRALVREPSAFLFDEPLSNLDAKLRVQMRV 175 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 E+++LQ L T++YVTHDQ EA+T+GDR+ VL+ G ++QVGTP++ Y +P ++FVA FI Sbjct: 176 EIKQLQRRLKTTSLYVTHDQLEALTLGDRLVVLNGGSIEQVGTPMEVYEKPASMFVATFI 235 Query: 241 GEPSMNLFDGSLSGDTFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQRT 300 G P+MN+ + + RG + D L + + +GIRP+D+ + Sbjct: 236 GSPAMNMLPVAYLRE--RG-------ANGLLDHLAADTDV-IGIRPDDLRIEAPDEDHLV 285 Query: 301 FDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHLFDG 360 V + E G E+ +++ D+ T T+ + V G+ A+H F+ Sbjct: 286 VTGTVELFEAAGAESHLYVSLEGSDQPT--VIRTSARPPVAEGETMRFHVLPSALHPFNQ 343 Query: 361 ETG 363 +G Sbjct: 344 ASG 346 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: 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: 354 Length adjustment: 30 Effective length of query: 353 Effective length of database: 324 Effective search space: 114372 Effective search space used: 114372 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