GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Pseudomonas putida KT2440

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate PP_1377 PP_1377 beta-ketoadipyl-CoA thiolase

Query= SwissProt::Q0AVM3
         (396 letters)



>FitnessBrowser__Putida:PP_1377
          Length = 400

 Score =  341 bits (874), Expect = 2e-98
 Identities = 180/398 (45%), Positives = 261/398 (65%), Gaps = 9/398 (2%)

Query: 4   EVVLVGACRTPVGTFGGTLKDVGSAQLGAIVMGEAIKR-AGIKAEQIDEVIFGCVLQAGL 62
           +V +  A RTP+G FGG L  V +  L A+ +   I+R  G++ +Q+DEV FGC  QAG 
Sbjct: 3   DVFICDAIRTPIGRFGGALASVRADDLAAVPLKALIERNPGVQWDQVDEVFFGCANQAGE 62

Query: 63  -GQNVARQCMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMDK 121
             +NVAR  ++ AG+P+ +   T+N++C SG+ AV  A + I +G+ ++++AGG E+M +
Sbjct: 63  DNRNVARMALLLAGLPESIPGVTLNRLCASGMDAVGTAFRAIASGEMELVIAGGVESMSR 122

Query: 122 APFILPNARWGYRMSMPKGDLIDEMVWGGLTDVFNGYH----MGITAENINDMYGITREE 177
           APF++  A   Y  +M   D    + W  +  +    +    M  TA+N+ D Y ++R +
Sbjct: 123 APFVMGKAESAYSRNMKLEDTT--IGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180

Query: 178 QDAFGFRSQTLAAQAIESGRFKDEIVPVVIKGKKGDIVFDTDEHPR-KSTPEAMAKLAPA 236
           QDAF  RSQ  AA A  +G F +EIVPV I  KKG+I+ + DEH R ++T EA+ KL P 
Sbjct: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGEIIVERDEHLRPETTLEALTKLKPV 240

Query: 237 FKKGGSVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGLGPIP 296
                +VTAGNASG+ND AAA+I+ S     + G+ P A+V+  ASGGV P VMG+GP+P
Sbjct: 241 NGPDKTVTAGNASGVNDGAAAMILASAAAVKKHGLTPRARVLGMASGGVAPRVMGIGPVP 300

Query: 297 ASRKALEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKMEKVNVNGGAIAIGHPIGS 356
           A RK  E+ G+ + D D+IE NEAFA+Q +AV R+LG AD   +VN NGGAIA+GHP+G 
Sbjct: 301 AVRKLTERLGIAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM 360

Query: 357 SGARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIVE 394
           SGAR+++T L++++K G +KGLAT+C+G G G AL +E
Sbjct: 361 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIE 398


Lambda     K      H
   0.317    0.135    0.387 

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: 453
Number of extensions: 18
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: 396
Length of database: 400
Length adjustment: 31
Effective length of query: 365
Effective length of database: 369
Effective search space:   134685
Effective search space used:   134685
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