GapMind for catabolism of small carbon sources

 

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

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate PfGW456L13_4610 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)

Query= uniprot:Q1MCU2
         (292 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4610
          Length = 255

 Score =  259 bits (663), Expect = 3e-74
 Identities = 132/258 (51%), Positives = 179/258 (69%), Gaps = 9/258 (3%)

Query: 14  LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73
           +LKVE+LSM+FGGL+A+N  +   K   + ALIGPNGAGKTTVFNC+TGFYKP+ G I  
Sbjct: 5   ILKVENLSMRFGGLLAVNGVALSVKEKQVVALIGPNGAGKTTVFNCLTGFYKPSGGSILL 64

Query: 74  NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTIL 133
           + ++     +E LP  +I  +  V RTFQN+RLF  +T +ENLL+AQH  L   +   + 
Sbjct: 65  DGEA-----IEGLPGHKIALKG-VVRTFQNVRLFKDMTAVENLLIAQHRHL---NTNFLS 115

Query: 134 GLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPELL 193
           GL     +++   EA++ A FWLEK +L + A+ PAG L YG QRRLEIAR M T P +L
Sbjct: 116 GLFKTPSFRKSEREAMDFAEFWLEKVNLKEFANRPAGTLAYGQQRRLEIARCMMTRPRIL 175

Query: 194 CLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKISD 253
            LDEPAAGLNP+E+  L AL+  +R E   ++LLIEHDM +VM ISDH+VV+  G  +++
Sbjct: 176 MLDEPAAGLNPKETEDLKALISMLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLAN 235

Query: 254 GTPDHVKNDPRVIAAYLG 271
           GTP+ ++++P VI AYLG
Sbjct: 236 GTPEQIRDNPEVIKAYLG 253


Lambda     K      H
   0.318    0.136    0.386 

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: 210
Number of extensions: 5
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: 292
Length of database: 255
Length adjustment: 25
Effective length of query: 267
Effective length of database: 230
Effective search space:    61410
Effective search space used:    61410
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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