GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Pseudomonas fluorescens FW300-N2C3

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate AO356_02325 AO356_02325 3-ketoacyl-CoA thiolase

Query= SwissProt::Q0AVM3
         (396 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_02325
          Length = 391

 Score =  289 bits (740), Expect = 8e-83
 Identities = 174/399 (43%), Positives = 251/399 (62%), Gaps = 22/399 (5%)

Query: 3   REVVLVGACRTPVG-TFGGTLKDVGSAQLGAIVMGEAIKR-AGIKAEQIDEVIFGCVLQA 60
           R+VV+V   RTP+G + GG  ++  +  + A ++ + ++R   +   ++++VI+GCV Q 
Sbjct: 6   RDVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNVKVDPNEVEDVIWGCVNQT 65

Query: 61  -GLGQNVARQCMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENM 119
              G N+AR   +   IP      T++++CGS + A+  AAQ I  G+ D+ + GG E+M
Sbjct: 66  LEQGWNIARMASLMTQIPHTAAGQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHM 125

Query: 120 DKAPFILPNARWGYRMSMPKGDLIDEMVWGGLTDVFNGYHMGITAENINDMYGITREEQD 179
                          +SM  G  +D      L        MG+TAE +  M+GI+RE+QD
Sbjct: 126 G-------------HVSMMHG--VDPNPHMSLYAAKASGMMGLTAEMLGKMHGISREQQD 170

Query: 180 AFGFRSQTLAAQAIESGRFKDEIVPVVIKGKKGDI-VFDTDEHPR-KSTPEAMAKLAPAF 237
           AFG RS  LA +A   G+FKDEI+P+    + G + +FD DE  R ++T E++A L PAF
Sbjct: 171 AFGVRSHQLAHKATVEGKFKDEIIPMQGYDENGFLKLFDYDETIRPETTLESLAALKPAF 230

Query: 238 K-KGGSVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGLGPIP 296
             KGG+VTAG +S I D A+ +IVMS ++A +LGI+PMA + S A  GVDP++MG GP+P
Sbjct: 231 NPKGGTVTAGTSSQITDGASCMIVMSAQRAQDLGIQPMAVIRSMAVAGVDPAIMGYGPVP 290

Query: 297 ASRKALEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKM-EKVNVNGGAIAIGHPIG 355
           A++KAL++AGL I DID  E NEAFAAQ++ V +DL   DKM EKVN++GGAIA+GHP G
Sbjct: 291 ATQKALKRAGLGIADIDFFELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFG 350

Query: 356 SSGARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIVE 394
            SGARI  TLL  M++ G   G++T+CIG G G A + E
Sbjct: 351 CSGARISGTLLNVMKQNGGTFGVSTMCIGLGQGIATVFE 389


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: 439
Number of extensions: 22
Number of successful extensions: 4
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: 391
Length adjustment: 31
Effective length of query: 365
Effective length of database: 360
Effective search space:   131400
Effective search space used:   131400
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