GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PPDCbeta in Echinicola vietnamensis KMM 6221, DSM 17526

Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate Echvi_3823 Echvi_3823 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit

Query= uniprot:G1UHX5
         (328 letters)



>FitnessBrowser__Cola:Echvi_3823
          Length = 326

 Score =  215 bits (548), Expect = 1e-60
 Identities = 123/327 (37%), Positives = 184/327 (56%), Gaps = 7/327 (2%)

Query: 1   MSEITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAE 60
           M EI   +AL  A+ + +R D    L GE++    G +++T G+  EFG +R  DTP++E
Sbjct: 1   MREIQFREALREAMSEEMRRDKNVFLMGEEVAEYNGAYKVTQGMLDEFGPDRVIDTPISE 60

Query: 61  SAILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYG 120
               G  VG  M G RP++E     F+  A +Q+V+  AK+   + GA  +P+  R P G
Sbjct: 61  GGFAGLGVGAGMNGLRPIIEFMTFNFSLVAIDQIVNSAAKMYAMSGGAYNVPIVFRGPTG 120

Query: 121 --GGIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLYW 178
             G +G    HS + E ++  TPGL VV P+   DA  LL+ +I   DPV+F+E + +Y 
Sbjct: 121 NAGQLGAT--HSSNFENWFANTPGLKVVVPSNPYDAKGLLKAAIRDDDPVIFMESELMYS 178

Query: 179 RKEALGLPVDTGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEVIDLRTL 238
            K  +       P+G A I+R G   T++++G  +  ALEAAE  A+ G + EVIDLRT+
Sbjct: 179 DKGEVPEGEYLLPIGVADIKRKGADVTIVSFGKIMKVALEAAEELAKDGIEAEVIDLRTV 238

Query: 239 MPLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDVP- 297
            P+D ATV  SV++T R VVV EA+  +    ++A  I +  F +L+APV RV   D+P 
Sbjct: 239 RPIDYATVYESVKKTNRCVVVEEANPISSLATDLAFNIQKNMFDYLDAPVLRVNSMDIPL 298

Query: 298 -YPPPLLERHYLPGVDRILDAVASLEW 323
            Y P  +E   LP V R ++AV  + +
Sbjct: 299 SYAPTYIEA-TLPNVKRTIEAVKQVTY 324


Lambda     K      H
   0.322    0.138    0.418 

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: 260
Number of extensions: 15
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: 328
Length of database: 326
Length adjustment: 28
Effective length of query: 300
Effective length of database: 298
Effective search space:    89400
Effective search space used:    89400
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 (21.9 bits)
S2: 48 (23.1 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