GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braG 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:Q1MCU3
         (247 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4610
           Branched-chain amino acid transport ATP-binding protein
           LivG (TC 3.A.1.4.1)
          Length = 255

 Score =  123 bits (309), Expect = 3e-33
 Identities = 78/248 (31%), Positives = 130/248 (52%), Gaps = 16/248 (6%)

Query: 11  LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70
           +L+V  +   +G + A+ GV + V + ++V+LIG NGAGK+T+   + G  +   GS++ 
Sbjct: 5   ILKVENLSMRFGGLLAVNGVALSVKEKQVVALIGPNGAGKTTVFNCLTGFYKPSGGSILL 64

Query: 71  EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMG----------AGLDNLKHF- 119
           +G  I  +P H+IA   + ++ +  R+F  MT +ENL +           +GL     F 
Sbjct: 65  DGEAIEGLPGHKIALKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFLSGLFKTPSFR 124

Query: 120 -----AEDVEKIFTLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGL 174
                A D  + +     LKE   +  GTL+ G+Q+ L I R +M RP++L+LDEP+ GL
Sbjct: 125 KSEREAMDFAEFWLEKVNLKEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184

Query: 175 APLIVKGIFEAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLAN 234
            P   + +   I  L E   +TV L+E +    + +S    V+  G    +G+ +++  N
Sbjct: 185 NPKETEDLKALISMLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLANGTPEQIRDN 244

Query: 235 PEVRAAYL 242
           PEV  AYL
Sbjct: 245 PEVIKAYL 252


Lambda     K      H
   0.320    0.137    0.387 

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: 158
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: 247
Length of database: 255
Length adjustment: 24
Effective length of query: 223
Effective length of database: 231
Effective search space:    51513
Effective search space used:    51513
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: 46 (22.3 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