GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdB in Pseudomonas putida KT2440

Align 2-oxoisovalerate dehydrogenase subunit beta; EC 1.2.4.4 (characterized)
to candidate PP_4402 PP_4402 branched-chain alpha-keto acid dehydrogenase complex, beta subunit

Query= CharProtDB::CH_121283
         (339 letters)



>FitnessBrowser__Putida:PP_4402
          Length = 339

 Score =  694 bits (1792), Expect = 0.0
 Identities = 336/339 (99%), Positives = 338/339 (99%)

Query: 1   MATTTMTMIQALRSAMDVMLERDDNVVVYGQDVGYFGGVFRCTEGLQTKYGKSRVFDAPI 60
           MATTTMTMIQALRSAMDVMLERDDNVVVYGQDVGYFGGVFRCTEGLQ KYGKSRVFDAPI
Sbjct: 1   MATTTMTMIQALRSAMDVMLERDDNVVVYGQDVGYFGGVFRCTEGLQNKYGKSRVFDAPI 60

Query: 61  SESGIVGTAVGMGAYGLRPVVEIQFADYFYPASDQIVSEMARLRYRSAGEFIAPLTLRMP 120
           SESGIVGTAVGMGAYGLRPVVEIQFADYFYPASDQIVSE+ARLRYRSAGEFIAPLTLRMP
Sbjct: 61  SESGIVGTAVGMGAYGLRPVVEIQFADYFYPASDQIVSELARLRYRSAGEFIAPLTLRMP 120

Query: 121 CGGGIYGGQTHSQSPEAMFTQVCGLRTVMPSNPYDAKGLLIASIECDDPVIFLEPKRLYN 180
           CGGGIYGGQTHSQSPEAMFTQVCGLRTVMPSNPYDAKGLLIASIECDDPVIFLEPKRLYN
Sbjct: 121 CGGGIYGGQTHSQSPEAMFTQVCGLRTVMPSNPYDAKGLLIASIECDDPVIFLEPKRLYN 180

Query: 181 GPFDGHHDRPVTPWSKHPHSAVPDGYYTVPLDKAAITRPGNDVSVLTYGTTVYVAQVAAE 240
           GPFDGHHDRPVTPWSKHPHSAVPDGYYTVPLDKAAITRPGNDV+VLTYGTTVYVAQVAAE
Sbjct: 181 GPFDGHHDRPVTPWSKHPHSAVPDGYYTVPLDKAAITRPGNDVTVLTYGTTVYVAQVAAE 240

Query: 241 ESGVDAEVIDLRSLWPLDLDTIVESVKKTGRCVVVHEATRTCGFGAELVSLVQEHCFHHL 300
           ESGVDAEVIDLRSLWPLDLDTIVESVKKTGRCVVVHEATRTCGFGAELVSLVQEHCFHHL
Sbjct: 241 ESGVDAEVIDLRSLWPLDLDTIVESVKKTGRCVVVHEATRTCGFGAELVSLVQEHCFHHL 300

Query: 301 EAPIERVTGWDTPYPHAQEWAYFPGPSRVGAALKKVMEV 339
           EAPIERVTGWDTPYPHAQEWAYFPGPSRVGAALKKVMEV
Sbjct: 301 EAPIERVTGWDTPYPHAQEWAYFPGPSRVGAALKKVMEV 339


Lambda     K      H
   0.320    0.137    0.424 

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: 584
Number of extensions: 7
Number of successful extensions: 1
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: 339
Length of database: 339
Length adjustment: 28
Effective length of query: 311
Effective length of database: 311
Effective search space:    96721
Effective search space used:    96721
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: 49 (23.5 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