GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Cupriavidus basilensis 4G11

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate RR42_RS07610 RR42_RS07610 acetyl-CoA acetyltransferase

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



>FitnessBrowser__Cup4G11:RR42_RS07610
          Length = 393

 Score =  323 bits (829), Expect = 4e-93
 Identities = 186/404 (46%), Positives = 261/404 (64%), Gaps = 17/404 (4%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           M D+ I  A RT +G+FGG+LA + A +L A+ +KA +E    V+ +QV EV  G    A
Sbjct: 1   MTDIVIVSAARTAVGKFGGSLAKIPAPELGAIVIKAALE-RAGVKPEQVSEVIMGQVLTA 59

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           G   +N AR A L AGLP  +P +T+N++C SG+ A+  A  AIA+G+ E+ +AGG E+M
Sbjct: 60  GS-GQNPARQAALKAGLPVMVPAMTINKVCGSGLKAVMLAANAIAAGDAEIVVAGGQENM 118

Query: 121 SRAPFVMGKAESGYSR-NMKLEDTTIG---WRFINPLMKSQYGVDSMPETADNVADDYQV 176
           S AP V+  +  G+   + KL D+ I    W   N     QY    M  TA+NVA +Y +
Sbjct: 119 SAAPHVLPGSRDGFRMGDAKLIDSMIVDGLWDVYN-----QY---HMGVTAENVAKEYGI 170

Query: 177 SRADQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIV-ERDEHLRPETTLEALT 235
           +R  QDAFA  SQ KA AAQ AG F EEIVPV I  +KG+ ++   DE +R   T +AL 
Sbjct: 171 TREAQDAFAAGSQNKAEAAQKAGKFDEEIVPVPIPQRKGDPVMFATDEFVRHGVTQDALA 230

Query: 236 KLKPVNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMG 295
            LKP      +VTA NASG+NDGAAA+++ SA   K+ GLTP A +    + GV P+VMG
Sbjct: 231 GLKPAFDKAGSVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIRAYGTAGVDPKVMG 290

Query: 296 IGPVPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALG 355
           +GPVPA ++   R G +V + D++E+NEAFA+Q LAV +++G   D  +VN NGGAIA+G
Sbjct: 291 MGPVPASKRCLSRAGWSVEELDLMEINEAFAAQALAVHKQMGW--DTSKVNVNGGAIAIG 348

Query: 356 HPLGMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIER 399
           HP+G SG R+++T LH++++    KGLA++C+G G G+ALA+ER
Sbjct: 349 HPIGASGCRILVTLLHEMKRRDAHKGLASLCIGGGMGVALAVER 392


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: 420
Number of extensions: 15
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 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