Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate WP_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC
Query= reanno::Dino:3607124 (338 letters) >NCBI__GCF_000759345.1:WP_043527041.1 Length = 354 Score = 317 bits (813), Expect = 2e-91 Identities = 174/345 (50%), Positives = 232/345 (67%), Gaps = 12/345 (3%) Query: 1 MAGIKIDKINKFY-GTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGR 59 MA I++ + K Y G +A+ I+L+I DGEFVV VGPSGCGKSTLLR +AGLE ++ G Sbjct: 1 MASIQLTGLKKTYAGNVEAVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETITDGT 60 Query: 60 IEIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAAR 119 ++I R V +EPA+RD+AMVFQ+YALYPHMTV N+ +G+K G + + + R+ +AA Sbjct: 61 LKIDDRVVNDLEPAERDIAMVFQNYALYPHMTVFGNLAYGLKNRGVKREEIERRVHDAAA 120 Query: 120 VLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGL 179 +L++E +L+RKP +LSGGQRQRVA+GRA+V+ PS FLFDEPLSNLDAKLRVQMRVE++ L Sbjct: 121 MLEIEPFLERKPRKLSGGQRQRVAMGRALVREPSAFLFDEPLSNLDAKLRVQMRVEIKQL 180 Query: 180 HKQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAM 239 ++L T +YVTHDQ+EA+T+ D++VVLN G IEQVG+PM++Y KP S FVA FIGSPAM Sbjct: 181 QRRLKTTSLYVTHDQLEALTLGDRLVVLNGGSIEQVGTPMEVYEKPASMFVATFIGSPAM 240 Query: 240 NVF-------SSDVGLQDISLDASAAFVGCRPEHIEIVPDGDGH--IAATVHVKERLGGE 290 N+ GL D L A +G RP+ + I + H + TV + E G E Sbjct: 241 NMLPVAYLRERGANGLLD-HLAADTDVIGIRPDDLRIEAPDEDHLVVTGTVELFEAAGAE 299 Query: 291 SLLYLGLKGGGQ-IVARVGGDDETKVGAAVSLRFSRHRLHQFDEA 334 S LY+ L+G Q V R G + LH F++A Sbjct: 300 SHLYVSLEGSDQPTVIRTSARPPVAEGETMRFHVLPSALHPFNQA 344 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: 354 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: 354 Length adjustment: 29 Effective length of query: 309 Effective length of database: 325 Effective search space: 100425 Effective search space used: 100425 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