Align GlpP, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate 3607126 Dshi_0548 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= TCDB::G3LHZ0 (288 letters) >FitnessBrowser__Dino:3607126 Length = 288 Score = 139 bits (350), Expect = 7e-38 Identities = 86/274 (31%), Positives = 146/274 (53%), Gaps = 14/274 (5%) Query: 15 PVLLLVAFSAVIPLM----TVVNYSVQDTFGNNEFFWAGTDWFVQTLHSDRFWESLQRNL 70 P ++ +A + PL+ T +++ EF W V T + FW+++ R Sbjct: 16 PAVIGLALVGIAPLLYALWTSLHFYNLTKLRRVEFIGLENYWTVLT--DEVFWQAMGRTF 73 Query: 71 LFSFIILALEIPLGIFIALNMPKSGPGVPVCLVLMALPLLIP----WNVVGTIWQVFGRV 126 L L+I LG+ IAL + + PG+ + L L L++P + VVG + QV Sbjct: 74 FLLGTALPLQIALGLGIALVLHQ--PGLTLVKTLARLSLVLPMATTYAVVGLLGQVMFNQ 131 Query: 127 DIGLLGHTLEAIGLDYNYVRDPIDAWVTVIVMDVWHWTSLVVLLCYAGLVSIPDAYYQAA 186 G++ L G D N++ DP +A+ +I DVW WT V L+ AGL +P +AA Sbjct: 132 KFGVVNQLLG--GADINWIGDPENAFAMIIFWDVWQWTPFVALVLLAGLTMVPGEVEEAA 189 Query: 187 KIDGASRWSVFRYIQLPKMKRVLLIAVLLRFMDSFMIYTEPFVVTGGGPGNSTTFLSIDL 246 +++ S+W+V RY+QLP + L+ ++LR D+ ++ F +T GGPG+ST F+S+ + Sbjct: 190 RLETKSKWTVLRYVQLPFLLPGLVAVLILRTADTLKLFDMVFTLTRGGPGSSTEFISLMI 249 Query: 247 VKMAVGQFDLGPAAAMSIIYFLIILLLSWVFYTV 280 ++ FD G A+A +II +I ++L+ ++ V Sbjct: 250 QRVGFRGFDQGLASAQAIILLIITIVLAQIYIRV 283 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: 279 Number of extensions: 19 Number of successful extensions: 4 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: 288 Length adjustment: 26 Effective length of query: 262 Effective length of database: 262 Effective search space: 68644 Effective search space used: 68644 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: 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