GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Azospirillum brasilense Sp245

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate AZOBR_RS20220 AZOBR_RS20220 acetyl-CoA acetyltransferase

Query= SwissProt::P50174
         (393 letters)



>FitnessBrowser__azobra:AZOBR_RS20220
          Length = 382

 Score =  280 bits (715), Expect = 6e-80
 Identities = 168/392 (42%), Positives = 241/392 (61%), Gaps = 18/392 (4%)

Query: 2   SNPSIVIASAARTAVGSFN-GAFGNTLAHELGAAAIKAVLERAGVEAGEVDEVILGQVLP 60
           +NP +VIA  AR+     N G        +L A  + A++ER GV   ++++V++G   P
Sbjct: 5   ANP-VVIAGYARSPFAFANKGELAKVRPDDLLAHVVAALVERTGVNPQDIEDVVVGCAFP 63

Query: 61  AGE-GQNPARQAAMKAGLPQEKTAWGMNQLCGSGLRAVALGMQQIATGDAKVIVAGGMES 119
            GE G N AR  +  A LP    A  +N+ CGS ++A+      I  G  +V + GG+ES
Sbjct: 64  EGEQGMNIARTVSFLAKLPLTAGATTINRYCGSSMQAIHQAAGAIQMGAGEVFLCGGIES 123

Query: 120 MSMAPHCAHLRGGVKMGDYKMIDTMIKDGLTDAFYGYHMGITAENVARKWQLTREEQDEF 179
           MS  P          MG   +    +KD   +A+    MG+TAENVAR+++++R +Q+  
Sbjct: 124 MSRVP---------MMGYNPLPHPGLKDHYPEAYCS--MGVTAENVARRYEISRADQEAM 172

Query: 180 ALASQNKAEAAQKAGRFADEIVPFVVKTRKGDVNVDQDEYIRHGATLDSIAKLRPAFDKE 239
           A  S  KA AAQ+AGR A+EIV   ++T  G   V++D  IR G + ++++ L+PAF  +
Sbjct: 173 AAESHAKAAAAQQAGRLAEEIV--AIQTAAG--LVERDGCIRPGTSGETLSGLKPAFLAD 228

Query: 240 GTVTAGNASGLNDGAAAALLMTEAEAARRGIQPLARIVSWATAGVDPQIMGTGPIPASRK 299
           G+VTAG +S L DGA+A L+ TEA A   G+  LARI S A AG  P++MG GP+PA++K
Sbjct: 229 GSVTAGTSSPLTDGASAVLVTTEAYAKANGLPILARIRSVAVAGCAPEVMGLGPVPAAQK 288

Query: 300 ALEKAGWSVADIELVEANEAFAAQACAVNKDLGWDPSIVNVNGGAIAIGHPIGASGARVL 359
           AL +AG S+ DI+++E NEAFAAQA A  +DL  DP+ VN++GGAIA+GHP+GA+GAR+ 
Sbjct: 289 ALARAGLSIRDIDVIELNEAFAAQAIACMRDLDIDPAKVNLDGGAIALGHPLGATGARIT 348

Query: 360 NTLLFEMKRRGVSKGLATLCIGGGMGVAMCVE 391
                 +KR G    LAT CIGGG G+A  +E
Sbjct: 349 GKAAALLKREGKQFALATQCIGGGQGIATVLE 380


Lambda     K      H
   0.317    0.132    0.381 

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: 362
Number of extensions: 22
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: 393
Length of database: 382
Length adjustment: 30
Effective length of query: 363
Effective length of database: 352
Effective search space:   127776
Effective search space used:   127776
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 (21.6 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