GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Pseudomonas fluorescens GW456-L13

Align High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate PfGW456L13_4610 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)

Query= TCDB::P21629
         (255 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4610
          Length = 255

 Score =  441 bits (1135), Expect = e-129
 Identities = 219/255 (85%), Positives = 239/255 (93%)

Query: 1   MSRPILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGG 60
           MSR IL+V  L+MRFGGLLAVNGV L V+EKQVV++IGPNGAGKTTVFNCLTGFY+P+GG
Sbjct: 1   MSREILKVENLSMRFGGLLAVNGVALSVKEKQVVALIGPNGAGKTTVFNCLTGFYKPSGG 60

Query: 61  LIRLDGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKT 120
            I LDGE I+GLPGHKIA KGVVRTFQNVRLFK+MTAVENLL+AQHRHLNTNFL+GLFKT
Sbjct: 61  SILLDGEAIEGLPGHKIALKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFLSGLFKT 120

Query: 121 PAFRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEP 180
           P+FR+SEREAM++A  WLE+VNL EFANR AGTLAYGQQRRLEIARCMMTRPRILMLDEP
Sbjct: 121 PSFRKSEREAMDFAEFWLEKVNLKEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEP 180

Query: 181 AAGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQ 240
           AAGLNPKET+DLKALI+ LR EHNVTVLLIEHDMKLVMSISDHIVVINQG PLA+GTPEQ
Sbjct: 181 AAGLNPKETEDLKALISMLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLANGTPEQ 240

Query: 241 IRDNPDVIKAYLGEA 255
           IRDNP+VIKAYLGEA
Sbjct: 241 IRDNPEVIKAYLGEA 255


Lambda     K      H
   0.320    0.137    0.391 

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: 299
Number of extensions: 5
Number of successful extensions: 1
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: 255
Length of database: 255
Length adjustment: 24
Effective length of query: 231
Effective length of database: 231
Effective search space:    53361
Effective search space used:    53361
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