Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_073038605.1 BUB04_RS08650 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= uniprot:D4GP39 (383 letters) >NCBI__GCF_900129305.1:WP_073038605.1 Length = 368 Score = 313 bits (802), Expect = 5e-90 Identities = 193/379 (50%), Positives = 238/379 (62%), Gaps = 27/379 (7%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA + LD V K + V + +L + D EF+VLVGPSGCGKSTTLRM+AGLE V Sbjct: 1 MAEIKLDQVNKRFKKNW-----VVRDFTLTVADKEFVVLVGPSGCGKSTTLRMIAGLEEV 55 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 T GE+ + RV+N V +DRDIAMVFQSYALYPH +V NM+FGL + G+P DEI +RV Sbjct: 56 TSGEISIGGRVVNHVPPKDRDIAMVFQSYALYPHMNVYKNMAFGLM-NRGVPRDEIDRRV 114 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 ++ ++LGISDLL R+P QLSGGQ+QRVA+GRAIVRDP+ FL DEPLSNLDAKLR +MR Sbjct: 115 KQAAEILGISDLLQRRPAQLSGGQRQRVAMGRAIVRDPQAFLFDEPLSNLDAKLRVQMRA 174 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 EL +L L T VYVTHDQ EAMT+ DR+ V+ DG++ QVG PL+ Y RP N FVAGFI Sbjct: 175 ELAKLHERLQSTIVYVTHDQIEAMTLADRIVVMKDGKIMQVGPPLEVYERPANRFVAGFI 234 Query: 241 GEPSMNLFDGSL---SGDTFRGDGFDYPLSGATRDQLGGASG-----LTLGIRPEDVTVG 292 G PSMN D L +GD + DG + L R + G + GIRPEDV Sbjct: 235 GSPSMNFLDVRLVEEAGDLW-VDGESFRLK-VPRHRAPAFRGHVNRPVIFGIRPEDVK-- 290 Query: 293 ER-----RSGQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTT 347 ER G AEV V EP G+E V + G FTA + V D Sbjct: 291 ERPGDALPEGVEPLRAEVDVREPIGSE--VIITATVGSHA--FTARISPNVAVRVHDPID 346 Query: 348 VSFPEDAIHLFDGETGDAL 366 ++ + +HLFD E+ AL Sbjct: 347 LAVNMNKMHLFDPESEQAL 365 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: 429 Number of extensions: 17 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: 368 Length adjustment: 30 Effective length of query: 353 Effective length of database: 338 Effective search space: 119314 Effective search space used: 119314 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