GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF 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)



>FitnessBrowser__azobra:AZOBR_RS20220
          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:

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