GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Rhizobium etli CFN 42

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_011427695.1 RHE_RS23190 acetyl-CoA C-acyltransferase

Query= metacyc::MONOMER-3207
         (400 letters)



>NCBI__GCF_000092045.1:WP_011427695.1
          Length = 395

 Score =  258 bits (659), Expect = 2e-73
 Identities = 153/396 (38%), Positives = 229/396 (57%), Gaps = 8/396 (2%)

Query: 4   VFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQAGED 63
           + I  A RTPIG F G L    A +L A  ++A +E +  V  + V+EV FGC   AG  
Sbjct: 7   IVIVGAARTPIGSFQGELKEATAPELGATAIRAALERS-RVPAEAVEEVVFGCVLPAGL- 64

Query: 64  NRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMSRA 123
            +  AR A + AGLP +    T+N++C SGM A+  A   IA+G   +A+AGG+ESM+ A
Sbjct: 65  GQAPARQAAISAGLPFATGSTTVNKMCGSGMKAVMMAHDLIAAGNASVAVAGGMESMTNA 124

Query: 124 PFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRADQDA 183
           P+++ +A  GY          +   F++ L  +      M   A++ A+ YQ +R  QD 
Sbjct: 125 PYLLDRARGGYRLG---HGRVVDHMFLDGLEDAYDKGRLMGSFAEDCAEAYQFTREAQDN 181

Query: 184 FALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKPVNGP 243
           +A+ S  +A  A A G F  EIV V +   K E +  RDE    +  ++ +  LKP    
Sbjct: 182 YAIASLTRAQKAIADGCFESEIVAVTVKSGKAEQVASRDEQ-PGKAKIDKIPTLKPAFRD 240

Query: 244 DKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVPAVR 303
             TVTA N+S ++DGAAAL+L      +  GL P A VLG A+   AP +    P+ A++
Sbjct: 241 GGTVTAANSSSISDGAAALVLMRRSEAEHRGLVPLATVLGHATHSQAPNLFATAPIGALQ 300

Query: 304 KLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGMSGA 363
           KL++R G+A+SD D+ E+NEAFA   +A +R+L +  +  +VN +GGA ALGHP+G SG 
Sbjct: 301 KLSDRTGLALSDVDLFEINEAFAVVAMAAMRDLDLPHE--KVNVHGGACALGHPIGASGG 358

Query: 364 RLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIER 399
           R+++T L  LE+   ++G+A +C+G G+  A+AIER
Sbjct: 359 RILVTLLSALERYDLKRGMAALCIGGGEATAVAIER 394


Lambda     K      H
   0.318    0.134    0.383 

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: 372
Number of extensions: 19
Number of successful extensions: 6
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: 400
Length of database: 395
Length adjustment: 31
Effective length of query: 369
Effective length of database: 364
Effective search space:   134316
Effective search space used:   134316
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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