GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PPDCbeta in Novosphingobium fuchskuhlense FNE08-7

Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate WP_067911130.1 AQZ52_RS12405 pyruvate dehydrogenase complex E1 component subunit beta

Query= uniprot:G1UHX5
         (328 letters)



>NCBI__GCF_001519075.1:WP_067911130.1
          Length = 454

 Score =  204 bits (519), Expect = 3e-57
 Identities = 124/320 (38%), Positives = 167/320 (52%), Gaps = 2/320 (0%)

Query: 1   MSEITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAE 60
           M   T+ +AL  A+ + +R D R  + GE++    G +++T GL  EFG  R  DTP+ E
Sbjct: 129 MVATTVREALRDAMAEEMRADDRVFVMGEEVAEYQGAYKVTQGLLEEFGPRRVIDTPITE 188

Query: 61  SAILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYG 120
               G   G AM G RP+VE     FA  A + +++  AK    + G +  P+  R P G
Sbjct: 189 YGFAGIGTGAAMGGLRPIVEFMTFNFAMQAIDHIINSAAKTNYMSGGQMRCPIVFRGPNG 248

Query: 121 GGIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLYWRK 180
                   HS +   +Y + PGL V+ P  AADA  LL+ +I S DPVVFLE + +Y R 
Sbjct: 249 AASRVGAQHSQNYAPWYASVPGLVVIAPYDAADAKGLLKSAIRSEDPVVFLENELVYGRT 308

Query: 181 -EALGLPVDTGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEVIDLRTLM 239
            +   L   T P+G A   R G   T+++Y   +  ALEAAE  A  G + EVIDLRTL 
Sbjct: 309 FDVPALDDYTVPIGKARTMRAGRDVTIVSYSIGIALALEAAEKLAAEGIEAEVIDLRTLR 368

Query: 240 PLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDVPYP 299
           PLD   V  S+ RT R VVV E        +EI + + E  F HL+APV RV   DVP P
Sbjct: 369 PLDKDAVLESLARTNRMVVVEEGFPVCSIASEIISLVMEEGFDHLDAPVLRVCNEDVPLP 428

Query: 300 -PPLLERHYLPGVDRILDAV 318
               LE+  L    R++ AV
Sbjct: 429 YAANLEKLALVDTARVIAAV 448


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: 429
Number of extensions: 29
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: 454
Length adjustment: 30
Effective length of query: 298
Effective length of database: 424
Effective search space:   126352
Effective search space used:   126352
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: 50 (23.9 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