GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Pseudomonas fluorescens FW300-N2E2

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate Pf6N2E2_2289 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

Query= SwissProt::Q0AVM3
         (396 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2289
          Length = 383

 Score =  286 bits (733), Expect = 5e-82
 Identities = 173/396 (43%), Positives = 248/396 (62%), Gaps = 22/396 (5%)

Query: 6   VLVGACRTPVG-TFGGTLKDVGSAQLGAIVMGEAIKR-AGIKAEQIDEVIFGCVLQA-GL 62
           V+V   RTP+G + GG  ++  +  + A ++ + ++R   +   ++++VI+GCV Q    
Sbjct: 1   VIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNVKVDPNEVEDVIWGCVNQTLEQ 60

Query: 63  GQNVARQCMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMDKA 122
           G N+AR   +   IP      T++++CGS + A+  AAQ I  G+ D+ + GG E+M   
Sbjct: 61  GWNIARMASLMTQIPHTAAGQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMG-- 118

Query: 123 PFILPNARWGYRMSMPKGDLIDEMVWGGLTDVFNGYHMGITAENINDMYGITREEQDAFG 182
                       +SM  G  +D      L        MG+TAE +  M+GITRE+QDAFG
Sbjct: 119 -----------HVSMMHG--VDPNPHMSLYAAKASGMMGLTAEMLGKMHGITREQQDAFG 165

Query: 183 FRSQTLAAQAIESGRFKDEIVPVVIKGKKGDI-VFDTDEHPR-KSTPEAMAKLAPAFK-K 239
            RS  LA +A   G+FKDEI+P+    + G + +FD DE  R ++T E++A L PAF  K
Sbjct: 166 VRSHQLAHKATVEGKFKDEIIPMQGYDENGFLKLFDYDETIRPETTLESLAALKPAFNPK 225

Query: 240 GGSVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGLGPIPASR 299
           GG+VTAG +S I D A+ +IVMS ++A +LGI+PMA + S A  GVDP++MG GP+PA++
Sbjct: 226 GGTVTAGTSSQITDGASCMIVMSAQRAQDLGIQPMAVIRSMAVAGVDPAIMGYGPVPATQ 285

Query: 300 KALEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKM-EKVNVNGGAIAIGHPIGSSG 358
           KAL++AGL I DID  E NEAFAAQ++ V +DL   DKM EKVN++GGAIA+GHP G SG
Sbjct: 286 KALKRAGLGIADIDFFELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSG 345

Query: 359 ARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIVE 394
           ARI  TLL  M++ G   G++T+CIG G G A + E
Sbjct: 346 ARISGTLLNVMKQNGGTFGVSTMCIGLGQGIATVFE 381


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: 430
Number of extensions: 18
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: 383
Length adjustment: 30
Effective length of query: 366
Effective length of database: 353
Effective search space:   129198
Effective search space used:   129198
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