Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate Pf1N1B4_3974 ABC transporter, ATP-binding protein
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3974 Length = 341 Score = 244 bits (624), Expect = 2e-69 Identities = 131/324 (40%), Positives = 197/324 (60%), Gaps = 3/324 (0%) Query: 1 MAGIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRI 60 MA ++++ + K YG A+ NL +E GEFV +GPSGCGK+T L+ +AG VSSGRI Sbjct: 1 MAFVQLENLGKRYGEIDAVVATNLSVEKGEFVSLLGPSGCGKTTTLQMIAGFVEVSSGRI 60 Query: 61 EIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARV 120 + GRD+T +PA R L +VFQSYAL+PHMTVR+N+ FG+++ D ++R+ ++ Sbjct: 61 VLDGRDITHAKPASRGLGVVFQSYALFPHMTVRDNVAFGLRMRKVPNDELQQRVDRVLKL 120 Query: 121 LQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLH 180 ++L + +R P +LSGGQRQRVA+ RA+V P V L DEPLSNLDA LR +M+ E+ + Sbjct: 121 VRLNQHAERYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDANLREEMQFEIRRIQ 180 Query: 181 KQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMN 240 +++G T + VTHDQ EA++++D++VV+ GRI Q+ +P LY P + F++ F+G + Sbjct: 181 REVGITTLMVTHDQSEALSISDRVVVMQAGRITQIDAPYTLYEHPRTEFISGFVGKANLL 240 Query: 241 VFSSDVG--LQDISLDASAAFVGCRPEHIEIVPDGDGHIAATVHVKERLGGESLLYLGLK 298 D +Q + D + RPE I++ G G + + + LG + L + Sbjct: 241 PGERDSAGVVQVCNRDNGELTLSLRPEKIDLRDVGLGRLQGKIVSRFFLGSQWLYGVSTS 300 Query: 299 -GGGQIVARVGGDDETKVGAAVSL 321 G +V R G G AV L Sbjct: 301 LGELSVVRRNDGSAPLIEGTAVGL 324 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: 309 Number of extensions: 11 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: 341 Length adjustment: 28 Effective length of query: 310 Effective length of database: 313 Effective search space: 97030 Effective search space used: 97030 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