GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Pseudomonas simiae WCS417

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate GFF1320 PS417_06710 beta-ketoadipyl CoA thiolase

Query= SwissProt::Q0AVM3
         (396 letters)



>FitnessBrowser__WCS417:GFF1320
          Length = 400

 Score =  326 bits (835), Expect = 8e-94
 Identities = 175/401 (43%), Positives = 253/401 (63%), Gaps = 9/401 (2%)

Query: 3   REVVLVGACRTPVGTFGGTLKDVGSAQLGAIVMGEAIKR-AGIKAEQIDEVIFGCVLQAG 61
           R+V +  A RTP+G FGG L  V +  L A+ +   I+R   +    +DEV  GC  QAG
Sbjct: 2   RDVFICDAIRTPIGRFGGGLSTVRADDLAALPIKALIERNPSVDWTAVDEVFLGCANQAG 61

Query: 62  L-GQNVARQCMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMD 120
              +NVAR  ++ AG+P+ +   T+N++C SG+ A+  A + I +G+ ++ +AGG E+M 
Sbjct: 62  EDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMS 121

Query: 121 KAPFILPNARWGYRMSMPKGDLIDEMVWGGLTDVFNGYH----MGITAENINDMYGITRE 176
           +APF++  A   +  +M   D    + W  +  +    +    M  TA+N+ D Y ++R 
Sbjct: 122 RAPFVMGKADAAFSRTMKLEDTT--IGWRFINPLMKAQYGVDAMPQTADNVADDYHVSRA 179

Query: 177 EQDAFGFRSQTLAAQAIESGRFKDEIVPVVIKGKKGDIVFDTDEHPRKSTP-EAMAKLAP 235
           +QDAF  RSQ   A A  +G F +EIVPV +  KKG+ V + DEHPR  T  EA+ KL P
Sbjct: 180 DQDAFALRSQQRTAAAQAAGFFAEEIVPVRVAHKKGETVVEQDEHPRADTTLEALTKLKP 239

Query: 236 AFKKGGSVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGLGPI 295
                 +VTAGNASG+ND AAA+I+ S E   + G+   A+V+  AS GV P VMG+GP+
Sbjct: 240 VNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTARARVLGMASAGVAPRVMGIGPV 299

Query: 296 PASRKALEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKMEKVNVNGGAIAIGHPIG 355
           PA RK +E+ GL + D D+IE NEAFA+Q +AV R+LG AD   +VN NGGAIA+GHP+G
Sbjct: 300 PAVRKLVERLGLAVTDFDVIELNEAFASQGLAVLRELGIADDAPQVNPNGGAIALGHPLG 359

Query: 356 SSGARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIVEAL 396
            SGAR+++T L++++K G  KGLAT+C+G G G AL +E +
Sbjct: 360 MSGARLVLTALHQLEKTGGSKGLATMCVGVGQGLALAIERI 400


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: 438
Number of extensions: 21
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