GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PPDCbeta in Sinorhizobium meliloti 1021

Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate SMc01031 SMc01031 pyruvate dehydrogenase subunit beta

Query= uniprot:G1UHX5
         (328 letters)



>FitnessBrowser__Smeli:SMc01031
          Length = 460

 Score =  221 bits (563), Expect = 3e-62
 Identities = 125/323 (38%), Positives = 182/323 (56%), Gaps = 2/323 (0%)

Query: 1   MSEITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAE 60
           M+ +T+ +AL  A+ + +R +    + GE++    G +++T GL  EFG  R  DTP+ E
Sbjct: 135 MATMTVREALRDAMAEEMRANEDVFVMGEEVAEYQGAYKVTQGLLQEFGARRVVDTPITE 194

Query: 61  SAILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYG 120
               G  VG AM G RP+VE     FA  A +Q+++  AK    + G +G P+  R P G
Sbjct: 195 HGFAGVGVGAAMTGLRPIVEFMTFNFAMQAIDQIINSAAKTLYMSGGQMGAPIVFRGPSG 254

Query: 121 GGIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLYWRK 180
                   HS     +Y   PGL VV P TAADA  LL+ +I  P+PV+FLE + LY + 
Sbjct: 255 AAARVAAQHSQCYAAWYSHIPGLKVVMPYTAADAKGLLKAAIRDPNPVIFLENEILYGQS 314

Query: 181 -EALGLPVDTGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEVIDLRTLM 239
            E   L     P+G A I R G  ATL+++G  +T A++AA      G D+E+IDLRT+ 
Sbjct: 315 FEVPKLDDFVLPIGKARIHRTGKDATLVSFGIGMTYAIKAAAELEAQGIDVEIIDLRTIR 374

Query: 240 PLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDVPYP 299
           P+D  TV  SV++TGR V V E +  +  G EIA R+ ++ F +L+AP+  + G DVP P
Sbjct: 375 PMDLPTVIESVKKTGRLVTVEEGYPQSSVGTEIATRVMQQAFDYLDAPILTIAGKDVPMP 434

Query: 300 -PPLLERHYLPGVDRILDAVASL 321
               LE+  LP V  ++DAV ++
Sbjct: 435 YAANLEKLALPNVAEVVDAVKAV 457


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: 364
Number of extensions: 24
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: 460
Length adjustment: 30
Effective length of query: 298
Effective length of database: 430
Effective search space:   128140
Effective search space used:   128140
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 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