Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate SM_b20419 SM_b20419 glycerol-3-phosphate ABC transporter ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__Smeli:SM_b20419 Length = 349 Score = 326 bits (835), Expect = 7e-94 Identities = 183/362 (50%), Positives = 233/362 (64%), Gaps = 22/362 (6%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA +TL DV K Y GDI A+ +SL I DGEF+VLVGPSGCGKST LRM+AGLE++ Sbjct: 1 MATITLKDVHKTYH----GDIAAIRGVSLAIADGEFIVLVGPSGCGKSTLLRMIAGLESI 56 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 T GE+ + DRV+NG+ +RDIAMVFQ+YALYPH +VR N+S+GL+ + P +EI +R+ Sbjct: 57 TSGEISIGDRVVNGLEPSERDIAMVFQNYALYPHMTVRQNLSYGLK-NRNTPKEEIERRI 115 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 + L I LDRKP QLSGGQ+QRVA+GRAIVR+P FL DEPLSNLDAKLR +MR Sbjct: 116 AKAAKSLEIEPFLDRKPRQLSGGQRQRVAMGRAIVREPAAFLFDEPLSNLDAKLRVQMRV 175 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 E++RLQ LG T+VYVTHDQ EAMT+ DR+ VL+ G ++QVGTP++ Y P FVA FI Sbjct: 176 EIKRLQRALGTTSVYVTHDQLEAMTLADRLVVLNGGRIEQVGTPIELYENPATAFVATFI 235 Query: 241 GEPSMNLFDGSLSGDTFRGDGFDYPLSGATRDQLGGASGL-TLGIRPEDVTVGERRSGQR 299 G PSMNL D + + L G GL T+GIRPED+T+ G Sbjct: 236 GSPSMNLLDLNTGNAAWSAPA-----------ALVGKPGLATIGIRPEDITLAGDTDGGE 284 Query: 300 TFDAEVVV--VEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHL 357 F A V V VE G E+ VH +G+ G+SR+ + V+ ++H Sbjct: 285 RFRARVRVGAVELVGAESYVHGTLANGE---PLVFRVAGRSRMMIDEEVEVAAVAGSLHW 341 Query: 358 FD 359 FD Sbjct: 342 FD 343 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: 418 Number of extensions: 27 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: 349 Length adjustment: 30 Effective length of query: 353 Effective length of database: 319 Effective search space: 112607 Effective search space used: 112607 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 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