GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1693 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)



>FitnessBrowser__Putida:PP_2767
          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.

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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