GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Acidovorax sp. GW101-3H11

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate Ac3H11_3037 Fructose ABC transporter, ATP-binding component FrcA

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3037
          Length = 268

 Score =  328 bits (841), Expect = 7e-95
 Identities = 170/257 (66%), Positives = 213/257 (82%), Gaps = 4/257 (1%)

Query: 6   ILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRL 65
           ++ A+GLVKRYG+VTALD ADF+L  GEILAVIGDNGAGKSS+IKA+SGA  PDEGEI L
Sbjct: 13  VMQAKGLVKRYGQVTALDGADFELRAGEILAVIGDNGAGKSSLIKALSGATVPDEGEILL 72

Query: 66  EGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAA 125
           +G+ IQF+SP+EAR+AGIETVYQ+LA++PA++IA+N+FLGRE+R+PG++G   R LD+  
Sbjct: 73  DGQRIQFKSPIEARRAGIETVYQDLAVAPAMTIAENLFLGRELRRPGLLGTALRMLDKKK 132

Query: 126 MEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVK 185
           M +++ A+++EL  + I+++ QAVETLSGGQRQ VAVARAAAF   VVIMDEPTAALGVK
Sbjct: 133 MLEESVARMAEL-KVGIRSMTQAVETLSGGQRQCVAVARAAAFARHVVIMDEPTAALGVK 191

Query: 186 ESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVA 245
           E   VLELI  VR +GLP++LISHNMPHVFE+ADRIHI RLG+R  V+NPK  +MSD VA
Sbjct: 192 EGNMVLELIRRVRDKGLPVILISHNMPHVFEIADRIHIARLGKRAAVVNPKKISMSDTVA 251

Query: 246 FMTG---AKEPPREAIA 259
            MTG   A + P E +A
Sbjct: 252 VMTGAMAASDLPAECLA 268


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: 232
Number of extensions: 9
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: 260
Length of database: 268
Length adjustment: 25
Effective length of query: 235
Effective length of database: 243
Effective search space:    57105
Effective search space used:    57105
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.

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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