Align ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized)
to candidate Ac3H11_2064 ABC-type sugar transport system, permease component
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1895 (302 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2064 Length = 293 Score = 397 bits (1019), Expect = e-115 Identities = 179/289 (61%), Positives = 233/289 (80%) Query: 14 DALQRWLPKLVLAPSMLIVLVGFYGYIIWTFILSFTNSSFMPSYKWVGLQQYMRLMDNDR 73 + + WLPKLV+AP+ ++ YG ++W +LS T S +P+Y+W GL QY RL + DR Sbjct: 4 NTFETWLPKLVVAPAFVLGFAFIYGLMVWNGVLSLTVSRMLPNYEWAGLAQYERLWEMDR 63 Query: 74 WWVASKNLALFGGMFISISLVLGVFLAVLLDQRIRKEGFIRTVYLYPMALSMIVTGTAWK 133 WWVA KNL +FG ++ SL++GV LAVLLDQ+IR EG +RT+YLYPMALS +VTGTAWK Sbjct: 64 WWVALKNLGIFGVGYVGGSLLIGVVLAVLLDQKIRAEGALRTIYLYPMALSFVVTGTAWK 123 Query: 134 WLLNPGLGLDKMLRDWGWEGFRLDWLVDQDRVVYCLVIAAVWQASGFVMAMFLAGLRGVD 193 WLLNPGLG++KM+RDWG+ F WLVD + +YC+VIA +WQ++GF MA+FLAGLRG+D Sbjct: 124 WLLNPGLGIEKMVRDWGFPNFEFGWLVDTEMAIYCVVIAGIWQSAGFAMALFLAGLRGID 183 Query: 194 QSIIRAAQVDGASLPTIYLKIVLPSLRPVFFSAFMILAHIAIKSFDLVAAMTAGGPGYSS 253 SII+AAQVDGASLP IY +IVLP+LRPVFFS M+L+H+AIKSFDLV A+TAGGPG+++ Sbjct: 184 DSIIKAAQVDGASLPRIYWRIVLPALRPVFFSTLMVLSHLAIKSFDLVMALTAGGPGFAT 243 Query: 254 DLPAMFMYSFTFSRGQMGIGSASAMLMLGAVLTILVPYLYSELRGKRHD 302 D+PA FMY+ +FSRGQ+G+G+ASA +ML V +++PYLYSELR K HD Sbjct: 244 DVPATFMYTMSFSRGQIGLGAASATMMLATVAALVIPYLYSELRTKAHD 292 Lambda K H 0.329 0.141 0.448 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: 397 Number of extensions: 10 Number of successful extensions: 1 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: 302 Length of database: 293 Length adjustment: 26 Effective length of query: 276 Effective length of database: 267 Effective search space: 73692 Effective search space used: 73692 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