Align ABC transporter for D-Trehalose, permease component 2 (characterized)
to candidate Ac3H11_2942 Various polyols ABC transporter, permease component 2
Query= reanno::Smeli:SM_b20327 (276 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2942 Length = 279 Score = 128 bits (322), Expect = 1e-34 Identities = 83/275 (30%), Positives = 143/275 (52%), Gaps = 13/275 (4%) Query: 5 IAKRTAFYALVAVIILVAVFPFYYAILTSLKSGTALFRID----YWPTDISLANYAGIFS 60 +A RTA VA+++ FP + LT+ K+ + + PT L N+ + Sbjct: 14 LALRTAAAWGVALLLF---FPLGWLFLTAFKTELQAIAVPPLFVFTPT---LENFHEVQE 67 Query: 61 HGTFVRNLGNSLLVATLVVAISLLLAVTAAYALARVRFRGRGLLLLTILSVSMFPQIAVL 120 ++ NS++ + L + L+LA AAYA+A + + +L+ +LS M P + L Sbjct: 68 RSDYLLYAKNSVITSVLSTVLGLMLAAPAAYAMAFFKGKYTKDILMWMLSTKMMPAVGAL 127 Query: 121 AGLFELIRFVGIFNTPLALIFSYMIFTLPFTVWVLTTFMRDLPIEIEEAAIVDGASPWVV 180 ++ L + + +T LALI + + LP VW+L + +D+P EI EAA +DGA+ W Sbjct: 128 VPIYVLAQKSHLLDTQLALIIVFALSNLPIMVWMLYSHFKDIPHEILEAARMDGATLWQE 187 Query: 181 ITRVFMPLMWPALVTTGLLAFIAAWNEFLFALTFTSSNTQRTVPVAIALLSGGSQFEIPW 240 + V +PL L +TGLL + +WNE ++L +++ + +A + S S + W Sbjct: 188 VRLVLLPLGMGGLASTGLLCLVLSWNEAFWSLNLSAA---KAGTLATLIASYSSPEGLFW 244 Query: 241 GNIMAASVIVTVPLVVLVLIFQRRIISGLTAGGVK 275 + AAS++ P+VV Q++++ GLT G VK Sbjct: 245 AKLSAASLMAIAPIVVFGWFSQKQLVQGLTFGAVK 279 Lambda K H 0.332 0.143 0.426 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: 165 Number of extensions: 7 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: 276 Length of database: 279 Length adjustment: 25 Effective length of query: 251 Effective length of database: 254 Effective search space: 63754 Effective search space used: 63754 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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