Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate RR42_RS12955 RR42_RS12955 glycerol-3-phosphate ABC transporter ATP-binding protein
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__Cup4G11:RR42_RS12955 Length = 367 Score = 313 bits (801), Expect = 6e-90 Identities = 170/366 (46%), Positives = 235/366 (64%), Gaps = 29/366 (7%) Query: 1 MAGIKIDKINKFY-GTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGR 59 MA + + + K Y G + + I+++I DGEF+V VGPSGCGKSTLLR +AGLE +S G Sbjct: 1 MAKLSLRNVQKTYAGNVKVVHGIDMEINDGEFIVIVGPSGCGKSTLLRMVAGLEAISGGE 60 Query: 60 IEIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAAR 119 + IG + V +EPA+RD+AMVFQ+YALYPHM+V +NM +G+K+ G + ++R+ AA Sbjct: 61 VHIGDKVVNHLEPAERDIAMVFQNYALYPHMSVYDNMAYGLKIRGMDKSEIEQRVKHAAG 120 Query: 120 VLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGL 179 +L+L L+RKP LSGGQRQRVA+GRAIV+ P+VFLFDEPLSNLDAKLRVQMR+EL+ L Sbjct: 121 ILELAPLLERKPRALSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDAKLRVQMRLELKEL 180 Query: 180 HKQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAM 239 H++L T +YVTHDQVEAMT+AD+++VLN G +EQ+G+P+++Y +P S FVA FIGSP M Sbjct: 181 HRRLRTTSMYVTHDQVEAMTLADRMMVLNGGSVEQIGTPLEVYARPASTFVASFIGSPPM 240 Query: 240 NVF-------------------------SSDVGLQDISLD-ASAAFVGCRPEHIEIVPDG 273 N+ + +G + L A +G RPEHIE Sbjct: 241 NLVPVTRTNGGQGEAQMRVEQKPGAQGAPATLGHLPMGLHLPERALLGLRPEHIEPCAAH 300 Query: 274 DGHIAATVHVKERLGGESLLYLGLKGGGQIVARVGGDDETKVGAAVSLRFSRHRLHQFD- 332 + V + E LG +S Y G GG +V R+ + G + + + LH FD Sbjct: 301 EAIAEIEVRLVEALGADSYAY-GTLGGQPVVVRLDSNMPVSSGDRLPITAAAEHLHFFDA 359 Query: 333 EAGRAI 338 ++G+ I Sbjct: 360 DSGKRI 365 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: 384 Number of extensions: 19 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 338 Length of database: 367 Length adjustment: 29 Effective length of query: 309 Effective length of database: 338 Effective search space: 104442 Effective search space used: 104442 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