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 15519 b1397 acetyl-CoA acetyltransferase (NCBI)

Query= SwissProt::Q0AVM3
         (396 letters)



>lcl|FitnessBrowser__Keio:15519 b1397 acetyl-CoA acetyltransferase
           (NCBI)
          Length = 401

 Score =  330 bits (847), Expect = 3e-95
 Identities = 181/401 (45%), Positives = 260/401 (64%), Gaps = 12/401 (2%)

Query: 3   REVVLVGACRTPVGTFGGTLKDVGSAQLGAIVMGEAIKR-AGIKAEQIDEVIFGCVLQAG 61
           RE  +    RTP+G +GG L  V +  L AI + E + R   + AE ID+VI GC  QAG
Sbjct: 2   REAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQAG 61

Query: 62  L-GQNVARQCMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMD 120
              +NVAR   + AG+P+ V+  TIN++CGSGL A+  AA+ IKAGD D+++AGG E+M 
Sbjct: 62  EDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMS 121

Query: 121 KAPFILPNARWGYRMSMPKGDLIDEMV-WGGLTDV----FNGYHMGITAENINDMYGITR 175
           +APF++  A   +     + ++ D  + W  +  +    F    M  TAEN+ ++  I+R
Sbjct: 122 RAPFVMGKAASAFSR---QAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISR 178

Query: 176 EEQDAFGFRSQTLAAQAIESGRFKDEIVPVVIKGKKGDIV-FDTDEHPR-KSTPEAMAKL 233
           E+QD+F  RSQ   A+A  SG   +EIVPVV+K KKG +     DEH R ++T E +  L
Sbjct: 179 EDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGL 238

Query: 234 APAFKKGGSVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGLG 293
              F+  G +TAGNASG+ND AAA+I+ S++ A   G+ P A++V+ A+ GV+P +MGLG
Sbjct: 239 KAPFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLG 298

Query: 294 PIPASRKALEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKMEKVNVNGGAIAIGHP 353
           P+PA+R+ LE+AGL+I D+D+IE NEAFAAQ++ V R+LG  D    VN NGGAIA+GHP
Sbjct: 299 PVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHP 358

Query: 354 IGSSGARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIVE 394
           +G SGAR+ +   +E+ +R  +  L T+CIG G G A+I+E
Sbjct: 359 LGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILE 399


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: 448
Number of extensions: 19
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: 401
Length adjustment: 31
Effective length of query: 365
Effective length of database: 370
Effective search space:   135050
Effective search space used:   135050
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