Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate SM_b20419 SM_b20419 glycerol-3-phosphate ABC transporter ATP-binding protein
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__Smeli:SM_b20419 Length = 349 Score = 336 bits (861), Expect = 6e-97 Identities = 182/349 (52%), Positives = 236/349 (67%), Gaps = 11/349 (3%) Query: 1 MAGIKIDKINKFY-GTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGR 59 MA I + ++K Y G A+ ++L I DGEF+V VGPSGCGKSTLLR +AGLE ++SG Sbjct: 1 MATITLKDVHKTYHGDIAAIRGVSLAIADGEFIVLVGPSGCGKSTLLRMIAGLESITSGE 60 Query: 60 IEIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAAR 119 I IG R V +EP++RD+AMVFQ+YALYPHMTVR+N+ +G+K + + RIA+AA+ Sbjct: 61 ISIGDRVVNGLEPSERDIAMVFQNYALYPHMTVRQNLSYGLKNRNTPKEEIERRIAKAAK 120 Query: 120 VLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGL 179 L++E +LDRKP QLSGGQRQRVA+GRAIV+ P+ FLFDEPLSNLDAKLRVQMRVE++ L Sbjct: 121 SLEIEPFLDRKPRQLSGGQRQRVAMGRAIVREPAAFLFDEPLSNLDAKLRVQMRVEIKRL 180 Query: 180 HKQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAM 239 + LG T +YVTHDQ+EAMT+AD++VVLN GRIEQVG+P++LY P + FVA FIGSP+M Sbjct: 181 QRALGTTSVYVTHDQLEAMTLADRLVVLNGGRIEQVGTPIELYENPATAFVATFIGSPSM 240 Query: 240 NVFSSDVGLQDISLDAS------AAFVGCRPEHIEIVPDGDG----HIAATVHVKERLGG 289 N+ + G S A+ A +G RPE I + D DG V E +G Sbjct: 241 NLLDLNTGNAAWSAPAALVGKPGLATIGIRPEDITLAGDTDGGERFRARVRVGAVELVGA 300 Query: 290 ESLLYLGLKGGGQIVARVGGDDETKVGAAVSLRFSRHRLHQFDEAGRAI 338 ES ++ L G +V RV G + V + LH FD AGR + Sbjct: 301 ESYVHGTLANGEPLVFRVAGRSRMMIDEEVEVAAVAGSLHWFDAAGRRL 349 Lambda K H 0.320 0.139 0.396 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: 408 Number of extensions: 18 Number of successful extensions: 2 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: 338 Length of database: 349 Length adjustment: 29 Effective length of query: 309 Effective length of database: 320 Effective search space: 98880 Effective search space used: 98880 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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