GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livG in Pseudomonas putida KT2440

Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate PP_0616 PP_0616 Branched-chain amino acid ABC transporter, ATP binding protein

Query= uniprot:A0A159ZWS6
         (255 letters)



>lcl|FitnessBrowser__Putida:PP_0616 PP_0616 Branched-chain amino
           acid ABC transporter, ATP binding protein
          Length = 250

 Score =  171 bits (434), Expect = 1e-47
 Identities = 106/258 (41%), Positives = 152/258 (58%), Gaps = 12/258 (4%)

Query: 1   MSREILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGG 60
           MS  +L+  +L + +G   AV GV L V+   +  +IGPNGAGKT++F+CLTG  Q T G
Sbjct: 1   MSDYLLETRHLELAYGPFKAVAGVDLKVRAGTIHTIIGPNGAGKTSLFHCLTGERQATAG 60

Query: 61  TILLDGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENL-LIAQHRHLNTNFFAGLFK 119
            IL +G+ I   P H     G+ R+FQ   LF++++  ENL L AQ R        GL  
Sbjct: 61  KILFNGQDIIRKPSHGRVALGMARSFQLTSLFQNLSVRENLRLAAQGRD-------GLGA 113

Query: 120 TPAFRKSEREAMEY--AEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILML 177
              +R  E +   +  A+  L+++ L+  A   AG L++GQQR LE+   +  +P +LML
Sbjct: 114 LNFWRSVEHKRSHWNTADQVLERLKLSARAETLAGELSHGQQRVLEVGMSICAKPTLLML 173

Query: 178 DEPAAGLNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGT 237
           DEP +G+   +   +  LI  L  +H  TVLLIEH+M +VMSIS  I V++ G  L +GT
Sbjct: 174 DEPTSGMGIDDIPVMTDLISDLGRDH--TVLLIEHNMSIVMSISQRITVMSHGQILVEGT 231

Query: 238 PEQIRDNPEVIKAYLGEA 255
           PEQ+R++  V  AYLGEA
Sbjct: 232 PEQVRNDERVRTAYLGEA 249


Lambda     K      H
   0.321    0.138    0.398 

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: 170
Number of extensions: 7
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: 255
Length of database: 250
Length adjustment: 24
Effective length of query: 231
Effective length of database: 226
Effective search space:    52206
Effective search space used:    52206
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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