Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate BPHYT_RS35680 BPHYT_RS35680 sugar ABC transporter ATP-binding protein
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__BFirm:BPHYT_RS35680 Length = 360 Score = 315 bits (807), Expect = 1e-90 Identities = 182/362 (50%), Positives = 235/362 (64%), Gaps = 27/362 (7%) Query: 1 MAGIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRI 60 MA +++ I K YG TQ + I+LDI+DGEFVV VGPSGCGKSTL+R +AGLE +S G + Sbjct: 1 MAAVQLSGIFKRYGDTQVVHGIDLDIDDGEFVVLVGPSGCGKSTLMRMVAGLEEISGGDL 60 Query: 61 EIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARV 120 IGG ++ P R+++MVFQSYALYPH++V EN+ FG ++ K RI AA++ Sbjct: 61 MIGGTRANSLAPQQRNISMVFQSYALYPHLSVYENIAFGPRIRKESSASFKPRIEAAAKM 120 Query: 121 LQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLH 180 L L YLDR P LSGGQRQRVA+GRA+V+ PS+FLFDEPLSNLDAKLRVQMR E++ LH Sbjct: 121 LNLGGYLDRLPRALSGGQRQRVAMGRAVVREPSLFLFDEPLSNLDAKLRVQMRTEIKALH 180 Query: 181 KQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMN 240 ++L T+IYVTHDQ+EAMTMAD+IVV+N GRIEQ+G P++LY P + FVA F+GSP+MN Sbjct: 181 QRLKNTVIYVTHDQIEAMTMADRIVVMNAGRIEQIGRPLELYDHPANLFVASFLGSPSMN 240 Query: 241 ----VFSSDVGLQDISLD-------------ASAAF-----VGCRPEHIE-IVPDGDGHI 277 V +S Q ++L+ ASA +G RPEHIE + P D Sbjct: 241 FAEGVIASRAQGQGLALNLTGGGEIVLEGAPASAVVGAKVTLGVRPEHIETMTPTPDA-- 298 Query: 278 AATVHVKERLGGESLLYLGLKGGGQIVARVGGDDETKVGAAVSLRFSRHRLHQFD-EAGR 336 V V E G E+ LY G GG + + G V+LR +H FD E+GR Sbjct: 299 TMEVEVVEPTGAETHLY-GKIGGSTWCVTTRQRSKIEPGQRVTLRLPAEHIHLFDTESGR 357 Query: 337 AI 338 + Sbjct: 358 RL 359 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: 394 Number of extensions: 16 Number of successful extensions: 1 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: 360 Length adjustment: 29 Effective length of query: 309 Effective length of database: 331 Effective search space: 102279 Effective search space used: 102279 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