GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Sphingomonas koreensis DSMZ 15582

Align 3-ketoacyl-CoA thiolase B, peroxisomal; Acetyl-CoA acyltransferase B; Beta-ketothiolase B; Peroxisomal 3-oxoacyl-CoA thiolase B; EC 2.3.1.155; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate Ga0059261_2160 Ga0059261_2160 acetyl-CoA acetyltransferases

Query= SwissProt::P07871
         (424 letters)



>FitnessBrowser__Korea:Ga0059261_2160
          Length = 398

 Score =  288 bits (738), Expect = 2e-82
 Identities = 177/399 (44%), Positives = 239/399 (59%), Gaps = 16/399 (4%)

Query: 37  DVVVVHGRRTPIGRAGRGGFKDTTPDELLSAVLTAVLQDVKLKPECLGDISVGNVLQPGA 96
           +  +V   RT IG+A RG F  T    L   V+ A ++   + P  + DI  G   Q G 
Sbjct: 3   EAAIVSTARTGIGKAYRGAFNTTEAPVLAGHVMNAAVERAGVDPARIDDIFWGVGNQWGT 62

Query: 97  -GAAMARIAQFLSGIPETVPLSAVNRQCSSGLQAVANIAGGIRNGSYDIGMACGVESMTL 155
            G    R+A F +G+P++VP   ++R+C SGL A+A  A  I  G  DI ++ G+ES++L
Sbjct: 63  QGGNAGRMAVFAAGLPQSVPAFTLDRKCGSGLTALALAARSIIAGDIDIALSGGMESISL 122

Query: 156 S-ERGNPGNISSRLLENEKARDCLIPMGITSENVAERFGISRQKQDAFALASQQKAASAQ 214
           +  +  P   +  +L NE      +PM  T+E VAER+GISR +QD +   SQQ+A +  
Sbjct: 123 TVTKDAPRYANQSVLANEP--HAYMPMIETAEIVAERYGISRARQDEYGAMSQQRAEAGL 180

Query: 215 SKGCFRAEIVPVTT--TVLDDKGDR---KTITVSQDEGVRPSTTMEGLAKLKPAFKDGGS 269
           + G F  EI P+T    + D +G+R   + +TV+QDEG+R  TT E LA LK  +KDG  
Sbjct: 181 ASGAFAEEIAPITVEKAIFDKEGNRTGSERVTVTQDEGIRAGTTAEALAGLKTVWKDGQV 240

Query: 270 T------TAGNSSQVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAY 323
                  TAGN+SQ+SDGAAA ++  R+ AE  G  ILG+ R +   G  PD MGIGP +
Sbjct: 241 VKEGRHITAGNASQLSDGAAAQIVMDRAIAEAEGKEILGIYRGFQAAGCAPDEMGIGPVF 300

Query: 324 AIPAALQKAGLTVNDIDIFEINEAFASQALYCVEKLGIPAEKVNPLGGAIALGHPLGCTG 383
           AIP  L +AGL V DI ++E+NEAFASQ LYC + LGI  EK N  GGAIA+GHP G TG
Sbjct: 301 AIPKLLGRAGLEVADIGLWELNEAFASQCLYCRDTLGIDPEKYNVNGGAIAIGHPFGMTG 360

Query: 384 ARQVVTLLNELKRRGRRAYGVVSMCIGTGMGAAAVFEYP 422
           AR +   L E ++RG R + VVSMC   GMGAA +FE P
Sbjct: 361 ARLIGHALIEGRKRGVR-WVVVSMCTAGGMGAAGLFEIP 398


Lambda     K      H
   0.316    0.133    0.378 

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: 458
Number of extensions: 19
Number of successful extensions: 6
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: 424
Length of database: 398
Length adjustment: 31
Effective length of query: 393
Effective length of database: 367
Effective search space:   144231
Effective search space used:   144231
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