Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate Ac3H11_2942 Various polyols ABC transporter, permease component 2
Query= uniprot:D8IPH9 (270 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2942 Length = 279 Score = 128 bits (322), Expect = 1e-34 Identities = 79/262 (30%), Positives = 138/262 (52%), Gaps = 7/262 (2%) Query: 1 MGRLITR-CAVWGVGIVLVLVAVFPLLWALLNSVKTLLDIVTPTPRFLFTPTLENYRQVI 59 +G L R A WGV ++L FPL W L + KT L + P F+FTPTLEN+ +V Sbjct: 11 LGLLALRTAAAWGVALLLF----FPLGWLFLTAFKTELQAIAVPPLFVFTPTLENFHEVQ 66 Query: 60 GSPEVLVGLTNSAVIVGSAVLLGTFMGVPAAYVIARYHVPGKRDIQFFLLSLRFLPPVAV 119 + L+ NS + + +LG + PAAY +A + +DI ++LS + +P V Sbjct: 67 ERSDYLLYAKNSVITSVLSTVLGLMLAAPAAYAMAFFKGKYTKDILMWMLSTKMMPAVGA 126 Query: 120 AIPLIAIWVDLGLYDTRFSMIVTYLLTTLSTITWLSIPVFQRMPREIEEAATLDGYGPYA 179 +P+ + L DT+ ++I+ + L+ L + W+ F+ +P EI EAA +DG + Sbjct: 127 LVPIYVLAQKSHLLDTQLALIIVFALSNLPIMVWMLYSHFKDIPHEILEAARMDGATLWQ 186 Query: 180 VFWKIALPNCATTLLGGIIFSFVLVWNELMIALALTSSNSATLPVVASAFTSMGQEVPWG 239 + LP L + VL WNE +L L+++ + TL + ++++S + + W Sbjct: 187 EVRLVLLPLGMGGLASTGLLCLVLSWNEAFWSLNLSAAKAGTLATLIASYSS-PEGLFWA 245 Query: 240 VINASTVLLALPPLIFVGVLSR 261 ++A++ L+A+ P++ G S+ Sbjct: 246 KLSAAS-LMAIAPIVVFGWFSQ 266 Lambda K H 0.327 0.142 0.434 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: 210 Number of extensions: 14 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: 270 Length of database: 279 Length adjustment: 25 Effective length of query: 245 Effective length of database: 254 Effective search space: 62230 Effective search space used: 62230 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 (21.7 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