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 15519 b1397 acetyl-CoA acetyltransferase (NCBI)

Query= SwissProt::Q0AVM3
         (396 letters)



>FitnessBrowser__Keio:15519
          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:

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