GapMind for catabolism of small carbon sources

 

Aligments for a candidate for atoB in Escherichia coli BW25113

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate 16448 b2342 acetyl-CoA acetyltransferase (NCBI)

Query= SwissProt::Q0AVM3
         (396 letters)



>lcl|FitnessBrowser__Keio:16448 b2342 acetyl-CoA acetyltransferase
           (NCBI)
          Length = 436

 Score =  225 bits (574), Expect = 2e-63
 Identities = 150/422 (35%), Positives = 231/422 (54%), Gaps = 32/422 (7%)

Query: 5   VVLVGACRTPVGTFGGTLKDVGSAQLGAIVMGEAIKRAGIKAEQIDEVIFGCVLQAGLGQ 64
           + +V   RTP          + +  LG +V+GE + R+ I AE I++++FG V+Q     
Sbjct: 15  IAIVSGLRTPFARQATAFHGIPAVDLGKMVVGELLARSEIPAEVIEQLVFGQVVQMPEAP 74

Query: 65  NVARQCMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMDKAPF 124
           N+AR+ ++  G+     A+++++ C +  +AV+  A+ + AG     +AGG ++    P 
Sbjct: 75  NIAREIVLGTGMNVHTDAYSVSRACATSFQAVANVAESLMAGTIRAGIAGGADSSSVLPI 134

Query: 125 --------ILPNARWGYRMS-----MPKGDLIDEM-VWGGLTDVFNGYHMGITAENINDM 170
                   +L +      MS       +  L D M V   + +   G  MG TAE +   
Sbjct: 135 GVSKKLARVLVDVNKARTMSQRLKLFSRLRLRDLMPVPPAVAEYSTGLRMGDTAEQMAKT 194

Query: 171 YGITREEQDAFGFRSQTLAAQAIESGRFKDEIVPVVIKGKKGDIVFDTDEHPRKSTPEAM 230
           YGITRE+QDA   RS   AAQA   G+ K+E++   I   K  +V D +     S  +  
Sbjct: 195 YGITREQQDALAHRSHQRAAQAWSDGKLKEEVMTAFIPPYKQPLVEDNNIRGNSSLAD-Y 253

Query: 231 AKLAPAF-KKGGSVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDP-S 288
           AKL PAF +K G+VTA N++ + D AAAVI+M++ +A ELG+ P+  + SYA   +D   
Sbjct: 254 AKLRPAFDRKHGTVTAANSTPLTDGAAAVILMTESRAKELGLVPLGYLRSYAFTAIDVWQ 313

Query: 289 VMGLGPIPASRKALEKAGLTIDDIDLIEANEAFAAQSIA---------VARD-LGWADKM 338
            M LGP  ++  ALE+AGLT+ D+ LI+ +EAFAAQ++A          AR+ LG A   
Sbjct: 314 DMLLGPAWSTPLALERAGLTMSDLTLIDMHEAFAAQTLANIQLLGSERFAREALGRAHAT 373

Query: 339 -----EKVNVNGGAIAIGHPIGSSGARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIV 393
                 K NV GG+IA GHP  ++GAR++   L+E+++RG   GL T C  GG+G A+++
Sbjct: 374 GEVDDSKFNVLGGSIAYGHPFAATGARMITQTLHELRRRGGGFGLVTACAAGGLGAAMVL 433

Query: 394 EA 395
           EA
Sbjct: 434 EA 435


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: 440
Number of extensions: 18
Number of successful extensions: 5
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: 436
Length adjustment: 31
Effective length of query: 365
Effective length of database: 405
Effective search space:   147825
Effective search space used:   147825
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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