GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PPDCbeta in Dinoroseobacter shibae DFL-12

Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate 3607113 Dshi_0535 Transketolase central region (RefSeq)

Query= uniprot:G1UHX5
         (328 letters)



>FitnessBrowser__Dino:3607113
          Length = 327

 Score =  243 bits (620), Expect = 5e-69
 Identities = 141/318 (44%), Positives = 182/318 (57%), Gaps = 2/318 (0%)

Query: 1   MSEITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAE 60
           + + T   AL  AL +A+  D   I+ GE++G  GG + +T  L  EFG ER  DTP++E
Sbjct: 3   VQQTTYRDALRLALSEAMTKDENVIVMGEEVGRYGGAYGVTKDLIKEFGPERVIDTPISE 62

Query: 61  SAILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYG 120
           +AI+G AVG AM G RPV E+ +  F     +QL +  AK+R    G IG+P+ +R   G
Sbjct: 63  AAIVGAAVGAAMTGLRPVAELMYVDFIGMTMDQLANQAAKIRYMFGGQIGVPMVLRTQGG 122

Query: 121 GGIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLYWRK 180
            G      HS S E Y M TPGL +  PAT  DAY LLR+S+  PDPVVF+E K LY  K
Sbjct: 123 TGRSAGAQHSQSLEGYIMHTPGLRLAMPATVEDAYHLLRQSLQQPDPVVFIEHKGLYTMK 182

Query: 181 EALGLPVDTGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEA-AAEHGWDLEVIDLRTLM 239
            AL         G A + R G    ++ Y   V  ALEAAE  A  HG ++ V+DLRTL 
Sbjct: 183 GALDPDAAPAGWGEATVLREGDDLVIVTYSRQVHHALEAAETLAGAHGINVTVVDLRTLN 242

Query: 240 PLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDVPYP 299
           PLD  T+   V   GRA+VV E     G  AE++ARITE CF  LE PV RV G D+P  
Sbjct: 243 PLDFDTIRPLVEAAGRAMVVSEGVMTCGVAAELSARITEECFDFLEEPVVRVAGEDIPIS 302

Query: 300 -PPLLERHYLPGVDRILD 316
             PLLE++ +P  + I+D
Sbjct: 303 VSPLLEQNSVPTPELIVD 320


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: 287
Number of extensions: 12
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: 327
Length adjustment: 28
Effective length of query: 300
Effective length of database: 299
Effective search space:    89700
Effective search space used:    89700
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