GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livG in Pseudomonas putida KT2440

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate PP_2767 PP_2767 putative Branched-chain amino acid ABC transporter, ATP-binding protein

Query= uniprot:A0A165KC86
         (260 letters)



>lcl|FitnessBrowser__Putida:PP_2767 PP_2767 putative Branched-chain
           amino acid ABC transporter, ATP-binding protein
          Length = 277

 Score =  207 bits (527), Expect = 2e-58
 Identities = 108/253 (42%), Positives = 159/253 (62%), Gaps = 1/253 (0%)

Query: 5   SNEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAG 64
           SN  +L++ GIS  F G++A+SD+G ++  G++  LIGPNGAGK++  N+I G+Y    G
Sbjct: 2   SNLPLLELEGISLSFKGVKAISDIGFSVAEGEICALIGPNGAGKSSLLNIINGVYRAQQG 61

Query: 65  TFELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRT 124
               AG+       H  A+ GIARTFQNI LF  M+ L+NV+ GR+++  S       R 
Sbjct: 62  RIRFAGQQRRVMHPHAAARDGIARTFQNIALFKGMSVLDNVLTGRNLKRRSSWLEQALRI 121

Query: 125 KGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEP 184
                E+      A+ +++++ I  + D    TL YG Q+R+E+ARALA +P+L+ LDEP
Sbjct: 122 GRAPGEDDRQRAAAERVIEFLRIQPWRDEIVGTLPYGLQKRIELARALAAEPRLLLLDEP 181

Query: 185 AAGMNATEKVQLRELIDRI-RNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAE 243
            AGMNA EK ++   I  I R    T++LIEHD+ +VMG+   V VLDYG++I +G+P +
Sbjct: 182 MAGMNAEEKREMSRFIVEINREFGMTVVLIEHDIGVVMGISHHVVVLDYGRKIGDGSPEQ 241

Query: 244 VQKNEKVIEAYLG 256
           V++N  VI AYLG
Sbjct: 242 VRRNPDVIAAYLG 254


Lambda     K      H
   0.319    0.137    0.384 

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: 208
Number of extensions: 9
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: 260
Length of database: 277
Length adjustment: 25
Effective length of query: 235
Effective length of database: 252
Effective search space:    59220
Effective search space used:    59220
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 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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