Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_164924745.1 NGR_RS30975 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= uniprot:D4GP39 (383 letters) >NCBI__GCF_000018545.1:WP_164924745.1 Length = 355 Score = 310 bits (795), Expect = 3e-89 Identities = 174/367 (47%), Positives = 237/367 (64%), Gaps = 21/367 (5%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 M +T+ +VTK Y G + + ++S I+DGEF+VLVGPSGCGKST LRM+AGLE + Sbjct: 1 MTDVTIRNVTKRY-----GALTVIPQLSFRIEDGEFVVLVGPSGCGKSTLLRMLAGLEEI 55 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 + G+L + V+N A++RD+A+VFQ+YALYPH +V NM F L+ P EI +RV Sbjct: 56 SGGDLLMGADVINDRPAKERDMAIVFQNYALYPHMTVAENMGFALKLRKR-PRAEIDERV 114 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 ++ +LG+ LLDR P LSGGQ+QRVA+GRAIVRDP+VFL DEPLSNLDAKLR +MR Sbjct: 115 DKAAAILGLGKLLDRYPRALSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRA 174 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 E++ L L +TTVYVTHDQ EAMTM D++ V+++G ++Q+GTPL+ Y RP N+FVAGFI Sbjct: 175 EIKALHQRLKITTVYVTHDQIEAMTMADKIVVMNEGRVEQMGTPLELYDRPANIFVAGFI 234 Query: 241 GEPSMNLFDGSLSGDT----FRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRS 296 G PSMN +++ +G P+ G L G S +T GIRPE + +GE Sbjct: 235 GSPSMNFLPATVAATNGPLLKTPEGVALPIDGG--PTLTGRSEVTYGIRPEHLQLGE--- 289 Query: 297 GQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIH 356 AEVVVVEP G+E +++ G + A + V G++ ++ + H Sbjct: 290 --TGIPAEVVVVEPTGSETQLYVTV----GGREVVAVLRDRVDVRPGEKIWLTPRKGCAH 343 Query: 357 LFDGETG 363 LFD TG Sbjct: 344 LFDPNTG 350 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: 463 Number of extensions: 30 Number of successful extensions: 6 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: 355 Length adjustment: 30 Effective length of query: 353 Effective length of database: 325 Effective search space: 114725 Effective search space used: 114725 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