Align GlpP, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate SM_b21603 SM_b21603 sugar uptake ABC transporter permease
Query= TCDB::G3LHZ0 (288 letters) >FitnessBrowser__Smeli:SM_b21603 Length = 291 Score = 108 bits (270), Expect = 1e-28 Identities = 81/276 (29%), Positives = 138/276 (50%), Gaps = 12/276 (4%) Query: 16 VLLLVAFSAVIPLMTVVNYSVQDTFGNN--------EFFWAGTDWFVQTLHSDRFWESLQ 67 VL++ F VI +TV Y V F + E W G D +++ L+ F+ S+ Sbjct: 13 VLMITPF--VITYLTVFAYPVYKMFALSFTNAPLVGEGEWVGFDNYLKLLNQKLFFTSVW 70 Query: 68 RNLLFSFIILALEIPLGIFIALNMPK-SGPGVPVCLVLMALPLLIPWNVVGTIWQVFGRV 126 F + + +G+ +AL + + G + LVL LP ++P +VV IW+ Sbjct: 71 NTGYFVVLTVIPNTLIGLGLALMVVRLKGWLQSLILVLFFLPYILPVSVVTQIWEWVLDQ 130 Query: 127 DIGLLGHTLEAI-GLDYNYVRDPIDAWVTVIVMDVWHWTSLVVLLCYAGLVSIPDAYYQA 185 G+ H +E + G + RDP+ A V ++ +W +LL AGL +IP YY+A Sbjct: 131 QFGIAQHVIEFVTGRRISVFRDPLWAMPMVALVTIWWTNGFNLLLFIAGLRNIPTDYYEA 190 Query: 186 AKIDGASRWSVFRYIQLPKMKRVLLIAVLLRFMDSFMIYTEPFVVTGGGPGNSTTFLSID 245 A +DGA+RW F+ I P + V + + L+ + I+ + +++T GGP NST L Sbjct: 191 AMLDGATRWQCFKRITWPLIWPVTALVLTLQLILQLKIFDQVYLMTEGGPFNSTYVLLQL 250 Query: 246 LVKMAVGQFDLGPAAAMSIIYFLIILLLSWVFYTVM 281 + + A G +A+++ FLII+ +S + Y ++ Sbjct: 251 VYREAFRLNHGGLGSAVAVFLFLIIVTVSVLQYQLL 286 Lambda K H 0.329 0.143 0.464 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: 245 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: 288 Length of database: 291 Length adjustment: 26 Effective length of query: 262 Effective length of database: 265 Effective search space: 69430 Effective search space used: 69430 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 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