Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate RR42_RS18590 RR42_RS18590 hypothetical protein
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__Cup4G11:RR42_RS18590 Length = 359 Score = 300 bits (767), Expect = 5e-86 Identities = 158/316 (50%), Positives = 210/316 (66%), Gaps = 23/316 (7%) Query: 1 MAGIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRI 60 MA ++I I K++G+TQ + +++DI DG+F V VGPSGCGKSTLLR +AGLE +++G I Sbjct: 1 MASVQIRGIQKYFGSTQVIRGVDIDIADGQFTVLVGPSGCGKSTLLRMIAGLEEITTGEI 60 Query: 61 EIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARV 120 IG R V + P +RD+AMVFQ+YALYPHMTV +NM F +K+ + + K ++A+A+ + Sbjct: 61 AIGNRVVNRLPPKERDIAMVFQNYALYPHMTVYDNMAFSLKLAKGDKEEIKRKVAKASAI 120 Query: 121 LQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLH 180 L L+ L+R P QLSGGQRQRVA+GRAIV++P VFLFDEPLSNLDAKLRVQMR E++ LH Sbjct: 121 LGLDSLLERYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRAEIKELH 180 Query: 181 KQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMN 240 ++L T +YVTHDQ+EAMTMAD+IVV+ GR+EQ G P+ LY P++ FVA FIGSPAMN Sbjct: 181 QRLRTTSVYVTHDQIEAMTMADQIVVMRDGRVEQRGKPLALYDHPDNLFVAGFIGSPAMN 240 Query: 241 VF-------SSDVGLQ---------------DISLDASAAFVGCRPEHIEIVPDGDGHIA 278 D ++ D G RPEH+ + G G + Sbjct: 241 FVPGVLRRSGGDAAVEFPDGTRLPAPARFDATAGTDGQRVIYGVRPEHLTLGMPGQG-LQ 299 Query: 279 ATVHVKERLGGESLLY 294 V V E G + +Y Sbjct: 300 TRVSVVEPTGANTEIY 315 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: 355 Number of extensions: 13 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: 359 Length adjustment: 29 Effective length of query: 309 Effective length of database: 330 Effective search space: 101970 Effective search space used: 101970 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