Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate CA265_RS04200 CA265_RS04200 phosphonate ABC transporter ATP-binding protein
Query= TCDB::G3LHY9 (356 letters) >FitnessBrowser__Pedo557:CA265_RS04200 Length = 226 Score = 100 bits (249), Expect = 4e-26 Identities = 70/222 (31%), Positives = 119/222 (53%), Gaps = 10/222 (4%) Query: 4 ITLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQPSH 63 I L++I Y AN K K+Y L+ V G +++GPSG GK+TLLNII L +P++ Sbjct: 2 IQLNNIEKYY-AN-KGIKNYVLRLVTTSIKQGEFVSIMGPSGAGKSTLLNIIGMLEEPTY 59 Query: 64 GRILFDGKDVTNLSTQSR------NIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVD 117 G F G++VT+L+ + R +I VFQ + D MTVY+N+ PL + V A+ Sbjct: 60 GSYEFLGENVTSLNERKRIELYRNHIGFVFQAYHLIDEMTVYENIEAPLLYKKVGSAERA 119 Query: 118 RRVRDILEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKW 177 R+ D+L+ ++ + L+ Q+Q + + R L + IL DEP + Sbjct: 120 SRIADLLDRFNIVAKKDLFPNQLSGGQQQLVGIARALAAQP-SIILADEPTGNLQSAQAD 178 Query: 178 VLRSQLKRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQI 219 + + K+L+++ G T++ VTH + A + +++ + DG + Sbjct: 179 EIMTLFKKLNQEDGITIIQVTHSEKNA-QYGNRILHIADGVV 219 Lambda K H 0.321 0.137 0.405 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: 135 Number of extensions: 11 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: 356 Length of database: 226 Length adjustment: 26 Effective length of query: 330 Effective length of database: 200 Effective search space: 66000 Effective search space used: 66000 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: 47 (22.7 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