GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pimB in Dyella japonica UNC79MFTsu3.2

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate N515DRAFT_0938 N515DRAFT_0938 acetyl-CoA C-acetyltransferase

Query= metacyc::MONOMER-20679
         (395 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_0938 N515DRAFT_0938
           acetyl-CoA C-acetyltransferase
          Length = 394

 Score =  202 bits (514), Expect = 1e-56
 Identities = 141/406 (34%), Positives = 205/406 (50%), Gaps = 35/406 (8%)

Query: 5   VIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQGATG 64
           VI    RT IG ++ G         L   AI+ A+++AGI  ++V +V+MG  +     G
Sbjct: 7   VIAGAKRTAIG-SFLGQFTGVPTPVLGATAIKAALEQAGIAAQDVNEVLMGCVLPANL-G 64

Query: 65  GNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESISLVQ 124
              AR+A L+AGLP     TT+++ C SG++AI L    +      + V GG ES++   
Sbjct: 65  QAPARQAALKAGLPAAVGCTTVNKVCGSGMKAIMLGHDLIKAGSAAVVVAGGMESMT--- 121

Query: 125 NDKMNTFHAVDPALEAIKGDVYM----------------AMLDTAETVAKRYGISRERQD 168
               N  H V+       GD  +                AM    E  A +Y  +RE QD
Sbjct: 122 ----NAPHMVNARTGIRYGDGQLVDHMAWDGLTNPYDGKAMGVFGELCADKYHFTREEQD 177

Query: 169 EYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAE 228
            +++ES +R  AAQQ G F  EI P+          T A    D+ +  DE P     A+
Sbjct: 178 AFAIESVKRAQAAQQNGAFAGEIVPV----------TVAGRKGDVVVDTDEQPGRSDIAK 227

Query: 229 GLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPD 288
             +   A R E  TITA ++S +SDGA+A V++S   A A+GL+PL       ++  EP+
Sbjct: 228 VPSLKPAFRKENGTITAASSSSISDGAAAVVLLSADDAKARGLQPLARIVAHATHSQEPE 287

Query: 289 EMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISV 348
                PV A+ ++L + G  VDD+ L+E+NEAFAV  +    +LGI   KLNVNGGA ++
Sbjct: 288 WFTTAPVSAIQKVLDKAGWKVDDVDLFEVNEAFAVVAMAPMRELGIPHAKLNVNGGACAL 347

Query: 349 GHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394
           GHP G SG RL    L   + R  K  V ++C+GGG  +A   E++
Sbjct: 348 GHPIGASGTRLVVTLLNALQTRGLKRGVASLCIGGGEATAIAVELL 393


Lambda     K      H
   0.316    0.134    0.378 

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: 394
Number of extensions: 22
Number of successful extensions: 3
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: 395
Length of database: 394
Length adjustment: 31
Effective length of query: 364
Effective length of database: 363
Effective search space:   132132
Effective search space used:   132132
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 (21.6 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 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, 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