Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate Ac3H11_4785 Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4785 Length = 334 Score = 323 bits (828), Expect = 4e-93 Identities = 171/339 (50%), Positives = 228/339 (67%), Gaps = 15/339 (4%) Query: 1 MAGIKIDKINKFYG----TTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVS 56 MA + + I K YG Q + +N +++DGEFVV VGPSGCGKSTLLR +AGLE +S Sbjct: 1 MASLSLRNITKRYGHGPKANQVIHGVNAEVKDGEFVVIVGPSGCGKSTLLRMVAGLEEIS 60 Query: 57 SGRIEIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAE 116 G + IG R V +EPA RD+AMVFQ+YALYPHMT ENM +G+K+ D K R+ + Sbjct: 61 GGELRIGDRVVNDLEPAQRDIAMVFQNYALYPHMTNFENMAYGLKIAKVPKDEIKARVDK 120 Query: 117 AARVLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVEL 176 AA++L+L L+RKP +LSGGQRQRVA+GRAIV+ P VFLFDEPLSNLDAKLR Q R+E+ Sbjct: 121 AAKILELGHLLERKPRELSGGQRQRVAMGRAIVRQPQVFLFDEPLSNLDAKLRAQTRLEI 180 Query: 177 EGLHKQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGS 236 + LH++LG T ++VTHDQVEAMT+A +++V+N G +EQ G+P ++YH P + FVA FIGS Sbjct: 181 QKLHRELGITSLFVTHDQVEAMTLAQRMIVMNAGNMEQFGTPEEVYHTPATTFVASFIGS 240 Query: 237 PAMNVFSSDVGLQDISLDASAAFVGCRPEHIEIVPDGDGHIAATVHVKERLGGESLLYLG 296 P MN+ + G Q +G RPEH+++ +G A TV E LG E L+Y G Sbjct: 241 PPMNLLKNAPGAQ------PGTILGIRPEHLDVRSEG---WAVTVETVELLGAERLIY-G 290 Query: 297 LKGGGQIVARV-GGDDETKVGAAVSLRFSRHRLHQFDEA 334 G Q++ RV G + + + ++ RLH FD A Sbjct: 291 RINGEQVIVRVEEGTHSPEPDSVIHVQPRADRLHAFDAA 329 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: 341 Number of extensions: 12 Number of successful extensions: 3 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: 334 Length adjustment: 28 Effective length of query: 310 Effective length of database: 306 Effective search space: 94860 Effective search space used: 94860 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