GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Rhizobium etli CFN 42

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_011427695.1 RHE_RS23190 acetyl-CoA C-acyltransferase

Query= uniprot:A0A2Z5MFE9
         (400 letters)



>NCBI__GCF_000092045.1:WP_011427695.1
          Length = 395

 Score =  254 bits (648), Expect = 4e-72
 Identities = 153/394 (38%), Positives = 223/394 (56%), Gaps = 8/394 (2%)

Query: 6   ICDAIRTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQAGEDNR 65
           I  A RTPIG + G LK+  A +LGA  I+A ++R+  V   AV++V++GC   AG   +
Sbjct: 9   IVGAARTPIGSFQGELKEATAPELGATAIRAALERSR-VPAEAVEEVVFGCVLPAGL-GQ 66

Query: 66  NVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESMTRAPF 125
             AR +A+ AGLP      T+N++CGSGM AV  A   I AG A + +AGG+ESMT AP+
Sbjct: 67  APARQAAISAGLPFATGSTTVNKMCGSGMKAVMMAHDLIAAGNASVAVAGGMESMTNAPY 126

Query: 126 VMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRADQDAFA 185
           ++ +A   +      H   +   F++ L         M   AE+ AE +  +R  QD +A
Sbjct: 127 LLDRARGGYRLG---HGRVVDHMFLDGLEDAYDKGRLMGSFAEDCAEAYQFTREAQDNYA 183

Query: 186 LASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGVVRPDG 245
           +AS  +A +A  DG    EIV V +   K + +  + DE P +  ++ +  LK   R  G
Sbjct: 184 IASLTRAQKAIADGCFESEIVAVTVKSGKAEQV-ASRDEQPGKAKIDKIPTLKPAFRDGG 242

Query: 246 TVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAPATQKL 305
           TVTA N+S ++DGA AL++  +  AE  GL   A V+G AT    P +    P  A QKL
Sbjct: 243 TVTAANSSSISDGAAALVLMRRSEAEHRGLVPLATVLGHATHSQAPNLFATAPIGALQKL 302

Query: 306 LRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGASGARL 365
             + G+ L  +D+ E+NEAFA   +A +R L L  +  +VN +GGA ALGHP+GASG R+
Sbjct: 303 SDRTGLALSDVDLFEINEAFAVVAMAAMRDLDLPHE--KVNVHGGACALGHPIGASGGRI 360

Query: 366 VTTALHQLERSNGRFALCTMCIGVGQGIALVIER 399
           + T L  LER + +  +  +CIG G+  A+ IER
Sbjct: 361 LVTLLSALERYDLKRGMAALCIGGGEATAVAIER 394


Lambda     K      H
   0.319    0.134    0.386 

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: 358
Number of extensions: 19
Number of successful extensions: 5
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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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