GapMind for catabolism of small carbon sources

 

Aligments for a candidate for AZOBR_RS08245 in Pseudomonas fluorescens FW300-N2C3

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate AO356_05335 AO356_05335 ABC transporter ATP-binding protein

Query= uniprot:G8ALJ0
         (294 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05335 AO356_05335 ABC
           transporter ATP-binding protein
          Length = 255

 Score =  273 bits (699), Expect = 2e-78
 Identities = 138/259 (53%), Positives = 192/259 (74%), Gaps = 9/259 (3%)

Query: 11  LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70
           +L VE+L+MRFGGL+AVN V+ +    ++ A+IGPNGAGKTT+FNC+TGFY PT G + L
Sbjct: 5   ILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTILL 64

Query: 71  RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130
              DG+   ++ +PG+ I++K  V RTFQN+RLF  M+ +ENL++AQH  L   +    A
Sbjct: 65  ---DGEP--IQGLPGHHIARKG-VVRTFQNVRLFKDMTAVENLLIAQHRHL---NTNFFA 115

Query: 131 GLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVML 190
           GL   P++ ++EREA++ A+YWLD+V L EFA+  AG L YG QRRLEIAR M T P +L
Sbjct: 116 GLFKTPAFRKSEREAMEYAEYWLDKVNLTEFANRTAGTLAYGQQRRLEIARCMMTRPRIL 175

Query: 191 CLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250
            LDEPAAGLNP+E+ +L  L+  +R+EH + VLLIEHDM +VM+ISDH+VV++ G  ++D
Sbjct: 176 MLDEPAAGLNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLAD 235

Query: 251 GDPAFVKNDPAVIRAYLGE 269
           G P  ++++P VI+AYLGE
Sbjct: 236 GTPEQIRDNPEVIKAYLGE 254


Lambda     K      H
   0.319    0.137    0.397 

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: 216
Number of extensions: 6
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: 294
Length of database: 255
Length adjustment: 25
Effective length of query: 269
Effective length of database: 230
Effective search space:    61870
Effective search space used:    61870
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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