GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Sinorhizobium fredii NGR234

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_012709489.1 NGR_RS26100 acetyl-CoA C-acyltransferase

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



>NCBI__GCF_000018545.1:WP_012709489.1
          Length = 393

 Score =  253 bits (647), Expect = 5e-72
 Identities = 155/395 (39%), Positives = 223/395 (56%), Gaps = 11/395 (2%)

Query: 4   VFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQAGED 63
           V I  A RTP+G F G L  + A +L A+ LKA ++       D VDEV  G    AG  
Sbjct: 7   VVIVSAARTPMGAFQGGLKDLTAPELGAIALKAALD---RAGLDAVDEVMMGNVLPAGL- 62

Query: 64  NRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMSRA 123
            +N AR A L AGL +  P  T++++C SGM A+     A+ SG   +   GG+ESM+ A
Sbjct: 63  GQNPARQAALGAGLGQQTPSTTVSKVCGSGMKALMLGHDALISGSASVVGVGGMESMTNA 122

Query: 124 PFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRADQDA 183
           P+++ KA  G+    +L    +        ++  Y    M   A++ A  YQ SRADQDA
Sbjct: 123 PYLLPKARGGF----RLGHGEVKDHMFLDGLEDAYSGRLMGTYAEDTAQHYQFSRADQDA 178

Query: 184 FALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKPVNGP 243
           FALRS ++A  A     FA+EIV +    K+G   ++RDE        + + KLKP    
Sbjct: 179 FALRSLERALKAAEDKSFADEIVAITDGGKRGTANLDRDEQPTKADPAK-IPKLKPAFRD 237

Query: 244 DKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVPAVR 303
             +VTA N+S ++DGAAAL+L  A   ++ GLTP A V G A     P      P+ A+ 
Sbjct: 238 GGSVTAANSSSISDGAAALVLMRASEAERRGLTPLAIVAGHAGHAQEPAWFTTAPIGAID 297

Query: 304 KLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGMSGA 363
           KL E+LG       + E+NEAFA   +A +R+LG++DD   VN +GGA ALGHP+G SGA
Sbjct: 298 KLIEKLGWEKGSVGLYEINEAFAIVAMAAIRDLGLSDDI--VNIHGGACALGHPIGASGA 355

Query: 364 RLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIE 398
           R+V+T LH +  +G ++G+A++C+G G+  A+ +E
Sbjct: 356 RIVVTLLHAMRANGVKRGIASLCIGGGEATAVGLE 390


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: 424
Number of extensions: 20
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: 393
Length adjustment: 31
Effective length of query: 369
Effective length of database: 362
Effective search space:   133578
Effective search space used:   133578
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