Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate HSERO_RS22750 HSERO_RS22750 sugar ABC transporter ATP-binding protein
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__HerbieS:HSERO_RS22750 Length = 377 Score = 320 bits (821), Expect = 3e-92 Identities = 181/361 (50%), Positives = 230/361 (63%), Gaps = 24/361 (6%) Query: 1 MAGIKIDKINKFY-GTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGR 59 MA + I ++ K Y G L +NLDI DGEF V VGPSGCGKSTLLR L GLE +S G Sbjct: 1 MAHVNIKQLRKTYDGRADVLAGLNLDIRDGEFCVLVGPSGCGKSTLLRMLCGLEEISGGE 60 Query: 60 IEIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAAR 119 + IGG+ V + PA+R +AMVFQSYALYPHM V +NM FG+KV G RI AA Sbjct: 61 LAIGGQVVNHLPPAERGIAMVFQSYALYPHMNVYKNMAFGLKVAGNSKSDIDARIRHAAA 120 Query: 120 VLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGL 179 +L+++ L R P +LSGGQRQRVAIGRAIV+ P +FLFDEPLSNLDA LRVQ R+E+ L Sbjct: 121 ILKIDHLLQRLPRELSGGQRQRVAIGRAIVRQPRLFLFDEPLSNLDAALRVQTRLEIAKL 180 Query: 180 HKQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAM 239 H+QL AT++YVTHDQVEAMT+ DKIVV++ GRI+Q G+P++LY +P + FVA FIGSP M Sbjct: 181 HRQLAATIVYVTHDQVEAMTLGDKIVVMHEGRIQQAGTPLELYQQPQNLFVAGFIGSPKM 240 Query: 240 NVFS------SDVGLQ-----------DIS----LDASAAFVGCRPEHI-EIVPDGDGHI 277 N F D G+Q D+ +A +G R E I E + DG + Sbjct: 241 NFFQGVVTRCDDSGVQVEIAGGLRLLADVDPLGVTPGAAVTLGLRAEQIREGLGDGQ-PL 299 Query: 278 AATVHVKERLGGESLLYLGLKGGGQIVARVGGDDETKVGAAVSLRFSRHRLHQFDEAGRA 337 V++ E LG + LY+ L GG IV R G+ +G ++L H H FD G+A Sbjct: 300 HGVVNLVEHLGEANFLYVTLDGGHDIVVRGDGNRNVDIGQPIALSVHSHAFHLFDAQGQA 359 Query: 338 I 338 + Sbjct: 360 L 360 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: 393 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: 377 Length adjustment: 29 Effective length of query: 309 Effective length of database: 348 Effective search space: 107532 Effective search space used: 107532 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