Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate WP_106710281.1 CU102_RS06970 ABC transporter ATP-binding protein
Query= reanno::Dino:3607124 (338 letters) >NCBI__GCF_003010955.1:WP_106710281.1 Length = 333 Score = 331 bits (849), Expect = 1e-95 Identities = 177/339 (52%), Positives = 233/339 (68%), Gaps = 9/339 (2%) Query: 1 MAGIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRI 60 M +KI+ I K +G L I+L+++DGEFV+FVGPSGCGKSTLLR +AGLE +SG I Sbjct: 1 MGSLKIENIRKSFGHVDVLKGIDLEVKDGEFVIFVGPSGCGKSTLLRVIAGLEDATSGDI 60 Query: 61 EIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARV 120 I G+ V PA R +AMVFQ+YALYPH++VR+NM G+K G D KER A+ + Sbjct: 61 LIDGKKVNNTPPAKRGIAMVFQTYALYPHLSVRDNMGLGLKQAGKPADEIKERTGIASSM 120 Query: 121 LQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLH 180 L L++YL+R+P +LSGGQRQRVAIGRAIV+ P +FLFDEPLSNLDA LRV R+E+ LH Sbjct: 121 LSLDEYLERRPAELSGGQRQRVAIGRAIVREPQLFLFDEPLSNLDAALRVNTRLEIARLH 180 Query: 181 KQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMN 240 +QL ATMIYVTHDQVEAMT+ADKIVVLN+G+IEQVGSPM+LY+ P + FVA FIGSP MN Sbjct: 181 RQLKATMIYVTHDQVEAMTLADKIVVLNKGKIEQVGSPMELYNAPQTIFVAGFIGSPQMN 240 Query: 241 VF-SSDVGLQDISLDASAAFVGCRPEHIEIVPDGDGHIAATVHVKERLGGESLLYLGLKG 299 + ++ +G + A +G RPEHI++ + +HV E LG ++++YL Sbjct: 241 LIDAAKLG------QSGAKTIGIRPEHIQVSKTSGEWKGSVIHV-EHLGADTIIYL-QTD 292 Query: 300 GGQIVARVGGDDETKVGAAVSLRFSRHRLHQFDEAGRAI 338 G + R+ G+ V + R ++FD G+ I Sbjct: 293 FGPLTVRLFGEHNYDVDGVLYATPDAGRTYRFDNDGQVI 331 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: 379 Number of extensions: 10 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: 333 Length adjustment: 28 Effective length of query: 310 Effective length of database: 305 Effective search space: 94550 Effective search space used: 94550 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 24 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