GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Dyella japonica UNC79MFTsu3.2

Align Acetyl-CoA acetyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized)
to candidate N515DRAFT_3009 N515DRAFT_3009 acetyl-CoA C-acetyltransferase

Query= curated2:P44873
         (393 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3009
          Length = 427

 Score =  191 bits (486), Expect = 3e-53
 Identities = 137/431 (31%), Positives = 211/431 (48%), Gaps = 49/431 (11%)

Query: 2   ENVVIVSAVRTPIGSFNGALSSVSAVDLGAIVIQEAIKRANIESALVNEVIMGNVLQAGL 61
           + V ++  +R P    N A + V    +   V+   ++R  +    + EV MG V++   
Sbjct: 6   KRVGVIGGIRIPFCRNNTAYADVGNFGMSVKVLGALVERFRLHGEELGEVAMGAVIKHSS 65

Query: 62  GQNPARQAALKAGIEKEIPSLTINKVCGSGLKSVALGAQSIISGDADIVVVGGMENMSQA 121
             N AR+A L +G+    P +T  + CG+ L +  + A  I +G  +  + GG +  S  
Sbjct: 66  EWNLAREAVLSSGLAPTTPGITTARACGTSLDNAIIIANKIAAGQIEAGIAGGSDTTSDV 125

Query: 122 PYLLDSKVRQGV-----------KMGNLTLRDTMIE-----DGLTCASNHYHMGITAENI 165
           P +L  + R+ +           KM   T   ++ E      G+        MG   E +
Sbjct: 126 PIVLGERFRKRLLAINRAKGWQDKMAAFTRGFSLKELKPSFPGVAEPRTGMSMGDHCERM 185

Query: 166 AEQYGISRQAQDELALRSQTLASQAVQLGVFDKEIVPVMVKTRKGDIIVSRDEYPKADTT 225
           A+++ I R+AQD LAL S    + A + G F+  +VP      +G   + RD + +AD++
Sbjct: 186 AKEWHIGREAQDRLALESHQKLAAAYEAGFFEDLVVPF-----RG---LKRDGFLRADSS 237

Query: 226 AEGLAKLKPAFKK---EGTVTAGNASGINDGAAALILVSESKAHALGLKAIAKIRSYASG 282
            E L  LKPAF K    GT+TAGN++G++DGAAA++L S+  A   GLK  A        
Sbjct: 238 MEKLGTLKPAFDKISGHGTLTAGNSTGLSDGAAAVLLGSDEWAARRGLKVQAYFLDAEVA 297

Query: 283 GVDPSVMGLG----PVPATQKALKKAGINLDDIDLIEANEAFASQFL------------- 325
            VD  V G G    P  A  + L + G+ L D D  E +EAFA+Q L             
Sbjct: 298 AVD-FVHGEGLLMAPTVAVPRMLARHGLTLQDFDFYEIHEAFAAQVLCTLRAWESETYCR 356

Query: 326 ---GVGKDL-NLDMNKTNIHGGAIALGHPIGASGARILVTLLHNLIEKDKKLGLATLCIG 381
              G+ + L ++D  K N+HG ++A GHP  A+GARI+ TL   L EK    GL ++C  
Sbjct: 357 NRLGLEQPLGSIDPAKLNVHGSSLAAGHPFAATGARIVATLAKMLEEKGSGRGLISICTA 416

Query: 382 GGQGISMIVER 392
           GG G++ I+ER
Sbjct: 417 GGMGVTAILER 427


Lambda     K      H
   0.315    0.133    0.360 

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: 375
Number of extensions: 14
Number of successful extensions: 6
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: 393
Length of database: 427
Length adjustment: 31
Effective length of query: 362
Effective length of database: 396
Effective search space:   143352
Effective search space used:   143352
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: 42 (22.0 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