GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaJ1 in Azospirillum brasilense Sp245

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate AZOBR_RS20220 AZOBR_RS20220 acetyl-CoA acetyltransferase

Query= SwissProt::P0C7L2
         (401 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS20220 AZOBR_RS20220 acetyl-CoA
           acetyltransferase
          Length = 382

 Score =  283 bits (724), Expect = 6e-81
 Identities = 178/390 (45%), Positives = 235/390 (60%), Gaps = 38/390 (9%)

Query: 19  GALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQAGEDNRNVARMATLLAGLP 78
           G L+ VR DDL A  +  L+ R   ++ + I+DV++GCA   GE   N+AR  + LA LP
Sbjct: 24  GELAKVRPDDLLAHVVAALVERTG-VNPQDIEDVVVGCAFPEGEQGMNIARTVSFLAKLP 82

Query: 79  QSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMSRAPFVMGKAASAFSRQA 138
            +   TTINR CGS + A+  AA AI+ G G++ + GG+ESMSR P +MG          
Sbjct: 83  LTAGATTINRYCGSSMQAIHQAAGAIQMGAGEVFLCGGIESMSRVP-MMG---------- 131

Query: 139 EMFDTTIGWRFVNPLMAQQFGTDSMPE-------TAENVAELLKISREDQDSFALRSQQR 191
                       NPL       D  PE       TAENVA   +ISR DQ++ A  S  +
Sbjct: 132 -----------YNPLPHPGL-KDHYPEAYCSMGVTAENVARRYEISRADQEAMAAESHAK 179

Query: 192 TAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLKAPFRANGVITAG 251
            A AQ +G LAEEIV +  +   G+V   + D  +RP T+ E L GLK  F A+G +TAG
Sbjct: 180 AAAAQQAGRLAEEIVAI--QTAAGLV---ERDGCIRPGTSGETLSGLKPAFLADGSVTAG 234

Query: 252 NASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLGPVPATRRVLERAG 311
            +S + DGA+A+++ +E  A A GL   ARI ++A AG  P +MGLGPVPA ++ L RAG
Sbjct: 235 TSSPLTDGASAVLVTTEAYAKANGLPILARIRSVAVAGCAPEVMGLGPVPAAQKALARAG 294

Query: 312 LSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHPLGMSGARLALAAS 371
           LSI D+DVIELNEAFAAQA+  +R+L +  D   VN +GGAIALGHPLG +GAR+   A+
Sbjct: 295 LSIRDIDVIELNEAFAAQAIACMRDLDI--DPAKVNLDGGAIALGHPLGATGARITGKAA 352

Query: 372 HELHRRNGRYALCTMCIGVGQGIAMILERV 401
             L R   ++AL T CIG GQGIA +LE V
Sbjct: 353 ALLKREGKQFALATQCIGGGQGIATVLEAV 382


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: 435
Number of extensions: 17
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 401
Length of database: 382
Length adjustment: 31
Effective length of query: 370
Effective length of database: 351
Effective search space:   129870
Effective search space used:   129870
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 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