GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Acidovorax sp. GW101-3H11

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate Ac3H11_2303 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

Query= SwissProt::P0C7L2
         (401 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2303
          Length = 392

 Score =  310 bits (794), Expect = 5e-89
 Identities = 179/404 (44%), Positives = 250/404 (61%), Gaps = 16/404 (3%)

Query: 1   MREAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60
           M +  I    RT +G++GGAL+   A +L AI +RE + R   L ++ I +VI+G    A
Sbjct: 1   MEDIVIVSAARTAVGKFGGALAKTPASELGAIVIREAIAR-AGLSSDQIGEVIMGQVLAA 59

Query: 61  GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120
           G   +N AR A++ AG+ +     TIN +CGSGL A+  AA+A+  GD D+++AGG E+M
Sbjct: 60  GV-GQNPARQASMKAGVAKETPALTINAVCGSGLKAVMLAAQAVAWGDSDIVVAGGQENM 118

Query: 121 SRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQ----FGTDSMPETAENVAELLKI 176
           S AP V+       SR  +       W+ V+ ++       +    M  TAENVA+   I
Sbjct: 119 SLAPHVLNG-----SRDGQRMGD---WKMVDSMIVDGLWDVYNQYHMGITAENVAKAYGI 170

Query: 177 SREDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLR 236
           +R+ QD+ AL SQQ+ A AQ +G  A+EIV V L  KKG       DE+L  +T  E L 
Sbjct: 171 TRDMQDALALGSQQKAAAAQDAGKFADEIVGVSLAQKKGDPILFNADEYLNRKTNAEALA 230

Query: 237 GLKAPFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMG 296
           GL+  F   G +TAGNASG+NDGAAA+++ S + AAA GL P ARI A  T+G++P  MG
Sbjct: 231 GLRPAFDKAGSVTAGNASGLNDGAAAVVVMSAKKAAALGLKPLARIAAFGTSGLDPATMG 290

Query: 297 LGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALG 356
           +GPVPA+R+ L+RAG +  D+D+ ELNEAFAAQA  V +EL +  D   VN NGGAIA+G
Sbjct: 291 MGPVPASRKALQRAGWNAADVDLFELNEAFAAQACAVNKELAI--DPAKVNVNGGAIAIG 348

Query: 357 HPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILER 400
           HP+G SG R+ +   HE+ RR+ +  L  +CIG G G+++ LER
Sbjct: 349 HPIGASGCRILVTLLHEMQRRDAKKGLAALCIGGGMGVSLALER 392


Lambda     K      H
   0.319    0.135    0.384 

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: 431
Number of extensions: 14
Number of successful extensions: 4
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: 401
Length of database: 392
Length adjustment: 31
Effective length of query: 370
Effective length of database: 361
Effective search space:   133570
Effective search space used:   133570
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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