GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PPDCbeta in Lacinutrix algicola AKS293

Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate WP_055434954.1 ASC41_RS01930 pyruvate dehydrogenase complex E1 component subunit beta

Query= uniprot:G1UHX5
         (328 letters)



>NCBI__GCF_001418085.1:WP_055434954.1
          Length = 325

 Score =  201 bits (512), Expect = 2e-56
 Identities = 113/327 (34%), Positives = 178/327 (54%), Gaps = 5/327 (1%)

Query: 1   MSEITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAE 60
           M  I   +A+  A+ + +R D    L GE++    G ++ + G+  EFG +R  DTP+AE
Sbjct: 1   MKTIQFREAICEAMSEEMRRDESIYLMGEEVAEYNGAYKASKGMLDEFGAKRVIDTPIAE 60

Query: 61  SAILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYG 120
               G A+G  M G RP+VE     F+    +Q++++ AK+R  + G +  P+  R P G
Sbjct: 61  LGFAGIAIGSTMTGNRPIVEYMTFNFSLVGIDQIINNAAKIRQMSGGQLKCPIVFRGPTG 120

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

Query: 179 RKEALGLPVDTGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEVIDLRTL 238
            K  +     T PLG A I+R GT  T++++G  +  A +AA+  A+ G   E+IDLRT+
Sbjct: 179 DKGEVPEGEYTIPLGVADIKREGTDVTIVSFGKIIKEAYKAADELAKEGISCEIIDLRTV 238

Query: 239 MPLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDVPY 298
            PLD   V  SV++T R VV+ EA  F     E+   +    F +L+APV ++   D P 
Sbjct: 239 RPLDKEAVLKSVKKTNRLVVLEEAWPFGNVSTELTYIVQSEAFDYLDAPVVKINTADTPA 298

Query: 299 P-PPLLERHYLPGVDRILDAVASLEWE 324
           P  P+L   +LP    ++ AV  + ++
Sbjct: 299 PYSPVLLAEWLPDYTEVIKAVKKVMYK 325


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: 251
Number of extensions: 10
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: 328
Length of database: 325
Length adjustment: 28
Effective length of query: 300
Effective length of database: 297
Effective search space:    89100
Effective search space used:    89100
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 24 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