GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Dechlorosoma suillum PS

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate Dsui_1109 Dsui_1109 ABC-type branched-chain amino acid transport systems, ATPase component

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__PS:Dsui_1109
          Length = 266

 Score =  118 bits (296), Expect = 1e-31
 Identities = 83/238 (34%), Positives = 127/238 (53%), Gaps = 4/238 (1%)

Query: 4   EPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEI 63
           E IL  + +  R+G V AL    F++   EI A+IG NGAGKSSM+  I+G   P EG I
Sbjct: 13  EVILDLQNISLRFGGVKALTDISFNVKEHEIRAIIGPNGAGKSSMLNVINGVYHPQEGRI 72

Query: 64  RLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDR 123
              G+  +   P  A   GI   +QN+AL   +S+ DN+  GR  +      +    L R
Sbjct: 73  VFHGEERKKMEPHMAATQGIARTFQNIALFKGMSVLDNIMTGRITKMKCGFLEQALYLGR 132

Query: 124 AAMEKQA-RAKLSE-LGLMTIQNINQA-VETLSGGQRQGVAVARAAAFGSKVVIMDEPTA 180
           A  E+ A R K+ E +  + IQ+I +  V  L  G ++ V + RA A    ++++DEP A
Sbjct: 133 AQKEELAHREKVEEVIDFLEIQHIRKTPVGRLPYGLQKRVELGRALAAEPSLLLLDEPMA 192

Query: 181 ALGVKESRRVLELILDVRRR-GLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKD 237
            + V+E + +   ILDV  + G  IVLI H+M  V +++DR+ +   G+++    P D
Sbjct: 193 GMNVEEKQDMCRFILDVNDQFGTTIVLIEHDMGVVMDISDRMVVLDYGKKIGDGTPDD 250


Lambda     K      H
   0.321    0.136    0.383 

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: 156
Number of extensions: 8
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: 260
Length of database: 266
Length adjustment: 25
Effective length of query: 235
Effective length of database: 241
Effective search space:    56635
Effective search space used:    56635
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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.

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