GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlF in Pseudomonas fluorescens FW300-N2E2

Align ABC transporter for D-Sorbitol, permease component 2 (characterized)
to candidate Pf6N2E2_1647 Maltose/maltodextrin ABC transporter, permease protein MalF

Query= reanno::Phaeo:GFF1304
         (288 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1647
          Length = 321

 Score =  141 bits (355), Expect = 2e-38
 Identities = 88/291 (30%), Positives = 151/291 (51%), Gaps = 13/291 (4%)

Query: 9   AARIMMAPAVILLLGWMLVPLTMTLYFSFKKYLPLRGGDLGWVGFDNY--------ARFL 60
           AA + ++P ++ L      PL  T +FS         GD  +VG  NY        +  L
Sbjct: 29  AAWLFLSPMLLCLALVAAWPLLRTFWFSLTDASLADTGDATFVGLSNYLFHSSAGWSGIL 88

Query: 61  SSSAFWPSVQATLVIVGGVLAITVILGVFLALLLNQPMWGQGIVRILVIAPFFVMPTVSA 120
               +W +V+ TL      + + ++LG+ +ALLLN    G+ +VR L++ P+ +   VSA
Sbjct: 89  VDPQWWNAVRNTLHFTVVSVGLEIVLGLMVALLLNVKFTGRALVRALILIPWAIPTIVSA 148

Query: 121 LVWKNMFMDPVNGLFAHLWKAFGA--EPVSWLSEASLQ--SIILIVSWQWLPFATLILLT 176
            +W  M  D   G+  HL    G    P++W ++A L   ++I++  W+ +PF TL++L 
Sbjct: 149 KIWSWMLNDQF-GIINHLMLGLGLIDAPLAWTADADLSMWAVIIVDVWKTVPFVTLLMLA 207

Query: 177 AIQSLDSEQLEAAEMDGAPPVARFGYITLPHLSRAITVVVLIQTIFLLSIFAEIFVTTQG 236
           A+Q L S+  EAA +DG  PV  F ++TLP L  A+ V  + + +  L +F  I+V T  
Sbjct: 208 ALQMLPSDCYEAARVDGIHPVKVFWWVTLPLLMPALLVAAIFRILDSLRVFDVIYVLTSN 267

Query: 237 SFGTKTLTYLIYQRVLESQNVGLGSAGGVYAIILANIVAIFLMRIVGKNLD 287
           S  T +++    Q ++E Q+VG GSA      ++  ++A+  + +  + L+
Sbjct: 268 SSSTMSMSVYARQHLVEFQDVGYGSAASTLLFLVVAVIAMAYLYLGRRQLE 318


Lambda     K      H
   0.328    0.140    0.430 

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: 291
Number of extensions: 18
Number of successful extensions: 3
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: 321
Length adjustment: 27
Effective length of query: 261
Effective length of database: 294
Effective search space:    76734
Effective search space used:    76734
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.

Links

Downloads

Related tools

About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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