GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Methylocystis bryophila S285

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate WP_085770502.1 B1812_RS04380 ABC transporter ATP-binding protein

Query= SwissProt::Q9F9B0
         (260 letters)



>NCBI__GCF_002117405.1:WP_085770502.1
          Length = 293

 Score =  115 bits (288), Expect = 1e-30
 Identities = 80/235 (34%), Positives = 117/235 (49%), Gaps = 8/235 (3%)

Query: 16  YGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFRSP 75
           +G + AL   DF +  GEI ++IG NGAGKSS+I  I+G   PD G I+L+         
Sbjct: 44  FGGIQALSEIDFSVAAGEICSIIGPNGAGKSSLINVITGLYRPDWGRIQLDKNSFSRMPT 103

Query: 76  MEARQAGIETVYQNLALSPALSIADNMFLGREIRKPG-----IMGKWFRSLDRAAMEKQA 130
                 G+   +QNLAL   LS+ DN+ +GR           + G      DR A E   
Sbjct: 104 ERLASLGVARTFQNLALFRGLSVFDNIAVGRVSATRSHWLEQVFGLPRARADRLATEIIV 163

Query: 131 RAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRV 190
              L  LGL  ++  N+   TL  G ++ V +ARA A   +++++DEP A +   E   +
Sbjct: 164 EEMLVFLGLGQVR--NRIAGTLPYGMQKRVELARALAIRPRLLLLDEPMAGMTAGEKAEM 221

Query: 191 LELILDVRRR-GLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAV 244
            E I   R R G  IVLI H++  V E++DR+ +   GR++    P D    +AV
Sbjct: 222 GEFIQLTRDRFGASIVLIEHDIGVVMELSDRVAVLDYGRKIADGPPSDVMNDEAV 276


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: 169
Number of extensions: 10
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: 293
Length adjustment: 25
Effective length of query: 235
Effective length of database: 268
Effective search space:    62980
Effective search space used:    62980
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 Apr 09 2024. 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