Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= uniprot:D4GP39 (383 letters) >NCBI__GCF_000744815.1:WP_037573817.1 Length = 369 Score = 323 bits (828), Expect = 5e-93 Identities = 189/376 (50%), Positives = 240/376 (63%), Gaps = 15/376 (3%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA +T D T++Y GGD AV+ + L+I DGEFLVLVGPSGCGKST+LRM+AGLE V Sbjct: 1 MATVTYDKATRIYP---GGDKPAVDALDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDV 57 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 G +R+ +R + + +DRDIAMVFQ+YALYPH +V NM F L+ + G+ EIR +V Sbjct: 58 NNGAIRIGERDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIA-GVNKAEIRSKV 116 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 EE +L +++ LDRKP LSGGQ+QRVA+GRAIVR+P+VFLMDEPLSNLDAKLR RT Sbjct: 117 EEAAKILDLTEFLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRT 176 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 ++ LQ LG+TTVYVTHDQ EAMTMGDRVAVL DG LQQV TP + Y RP NLFVAGFI Sbjct: 177 QIAGLQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDTPRNMYDRPANLFVAGFI 236 Query: 241 GEPSMNLFDGSLSGDTFRGDGFDYPLSGATRDQLGGASG-----LTLGIRPE--DVTVGE 293 G P+MNL + + T G F + +RD +G A+ +T+G+RPE D+ G Sbjct: 237 GSPAMNLVEVPI---TDGGVKFGESVVQVSRDAVGEAANAGDKTVTVGVRPEHLDIVGGT 293 Query: 294 RRSGQ-RTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPE 352 G+ + V VVE G + V+ G E G+ GD+ V Sbjct: 294 EGGGEDKGLAVTVNVVEELGADGYVYGSAKVGTETIDLVVRVGGRDIPMKGDQLRVVPRA 353 Query: 353 DAIHLFDGETGDALKN 368 H+F TG L + Sbjct: 354 GETHVFSTSTGKRLSD 369 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: 485 Number of extensions: 28 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: 369 Length adjustment: 30 Effective length of query: 353 Effective length of database: 339 Effective search space: 119667 Effective search space used: 119667 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