GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pcaF 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)



>lcl|FitnessBrowser__Cup4G11:RR42_RS07610 RR42_RS07610 acetyl-CoA
           acetyltransferase
          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.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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