GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00895 in Pseudomonas putida KT2440

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate PP_4864 PP_4864 High-affinity branched-chain amino acid transport ATP-binding protein BraF

Query= uniprot:D8J1T6
         (255 letters)



>lcl|FitnessBrowser__Putida:PP_4864 PP_4864 High-affinity
           branched-chain amino acid transport ATP-binding protein
           BraF
          Length = 291

 Score =  205 bits (521), Expect = 1e-57
 Identities = 117/280 (41%), Positives = 168/280 (60%), Gaps = 31/280 (11%)

Query: 5   LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64
           +L + ++  +FGG++AL+ V + + R QI+ LIGPNGAGKTT FN +TG Y+   G  EL
Sbjct: 6   ILSVDNLMMQFGGIKALSDVSLKVRRNQIFALIGPNGAGKTTVFNCLTGFYKASGGRIEL 65

Query: 65  D------------GKPY------SPS------------APHEVAKAGIARTFQNIRLFGE 94
           +            G+ +      SP+              H V +AG+ARTFQNIRLF E
Sbjct: 66  NVRGSHTNVIQLLGERFQAADFVSPARFANRMYYKMFGGTHLVNRAGLARTFQNIRLFKE 125

Query: 95  MTVLENVMVGCHVRTKQNVFGAVFRHKAAREEEAAIREKSQKLLDFVGIGQFAKRTARHL 154
           M+V+EN++V  H+   +N+   V   KA R+ E+   + +   L+ V +   A R A  L
Sbjct: 126 MSVVENLLVAQHMWVNRNLLAGVLNTKAYRKAESDALDHAFYWLEVVDLVDCANRLAGEL 185

Query: 155 SYGDQRRLEIARALATDPQLLALDEPAAGMNATEKLGLRELLVKIQAEGK-TILLIEHDV 213
           SYG QRRLEIARA+ T P+++ LDEPAAG+N  E   L  ++  ++ E   T++LIEHD+
Sbjct: 186 SYGQQRRLEIARAMCTRPKIICLDEPAAGLNPQETEALSRMIRVLRDEHDITVVLIEHDM 245

Query: 214 KLMMGLCNRITVLDYGKPIAEGVPADVQKNPAVIEAYLGA 253
            ++M + + I VLD+G  IAEG P D++ NP VI AYLGA
Sbjct: 246 GMVMSISDHIVVLDHGNVIAEGAPQDIRHNPTVIAAYLGA 285


Lambda     K      H
   0.320    0.138    0.394 

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: 192
Number of extensions: 8
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: 291
Length adjustment: 25
Effective length of query: 230
Effective length of database: 266
Effective search space:    61180
Effective search space used:    61180
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 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, the preprint 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