GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Keio:16448
          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:

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