GapMind for catabolism of small carbon sources

 

Aligments for a candidate for atoB in Pseudomonas simiae WCS417

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate GFF1490 PS417_07580 3-ketoacyl-CoA thiolase

Query= SwissProt::Q0AVM3
         (396 letters)



>lcl|FitnessBrowser__WCS417:GFF1490 PS417_07580 3-ketoacyl-CoA
           thiolase
          Length = 391

 Score =  290 bits (741), Expect = 6e-83
 Identities = 174/399 (43%), Positives = 249/399 (62%), Gaps = 22/399 (5%)

Query: 3   REVVLVGACRTPVG-TFGGTLKDVGSAQLGAIVMGEAIKR-AGIKAEQIDEVIFGCVLQA 60
           R+VV+V   RTP+G + GG  ++  +  + A ++ + ++R   +   ++++VI+GCV Q 
Sbjct: 6   RDVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKVLERNTKVDPNEVEDVIWGCVNQT 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+GITRE QD
Sbjct: 126 G-------------HVSMMHG--VDPNPHMSLYAAKASGMMGLTAEMLGKMHGITREAQD 170

Query: 180 AFGFRSQTLAAQAIESGRFKDEIVPVVIKGKKGDI-VFDTDEHPRKSTP-EAMAKLAPAF 237
           AFG RS  LA +A   G+FKDEI+P+    + G + + D DE  R  T  E++A L PAF
Sbjct: 171 AFGLRSHQLAHKATLEGKFKDEIIPMNGYDENGFLKLCDYDETIRPDTTLESLAALKPAF 230

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

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

Query: 356 SSGARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIVE 394
            SGARI  TLL  M++ G   G+AT+CIG G G + + E
Sbjct: 351 CSGARISGTLLNVMKQNGGNLGVATMCIGLGQGISTVFE 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: 437
Number of extensions: 23
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.

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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