GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Sphingomonas koreensis DSMZ 15582

Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate Ga0059261_2888 Ga0059261_2888 acetyl-CoA acetyltransferases

Query= SwissProt::Q0KBP1
         (394 letters)



>FitnessBrowser__Korea:Ga0059261_2888
          Length = 393

 Score =  487 bits (1254), Expect = e-142
 Identities = 247/391 (63%), Positives = 303/391 (77%), Gaps = 1/391 (0%)

Query: 4   EVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQTEPR 63
           +V+++SGVRTAIG FGG+LK+V  A+LGALV+ EA+ARA ++ D VGHVV GNVI + P 
Sbjct: 3   DVLILSGVRTAIGDFGGALKNVPAADLGALVIGEAIARAGIAADAVGHVVMGNVIPSTPS 62

Query: 64  DMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESMSRA 123
           D YL RVAAV  GV +  PALTVNRLCGSGLQAI+SAAQ I LG+  VA+ GGAE+MS+A
Sbjct: 63  DAYLARVAAVRAGVPVAVPALTVNRLCGSGLQAIISAAQGIALGECGVAVAGGAENMSQA 122

Query: 124 PYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAALES 183
           P+   +AR+G +MGD  ++D +   L DPF ++HMGVTAENVA +  I RA QDEAA+ES
Sbjct: 123 PHYVASARFGQKMGDIQMLDALTRTLSDPFDQVHMGVTAENVAAQCGIDRAAQDEAAVES 182

Query: 184 HRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKENGTV 243
           HRR + AI  G F+DQIVPV  K R G V FDTDEHVR + T++DM +LRP F + +GTV
Sbjct: 183 HRRGARAIAEGRFRDQIVPVEIKSRGGTVMFDTDEHVRAEVTLEDMARLRPAF-QRDGTV 241

Query: 244 TAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKIALE 303
           TAGNASG+ND AAAVV+    EA+R G KPLAR++ +GHAGV+P+ MG+GPV A  IAL 
Sbjct: 242 TAGNASGINDGAAAVVLGSPEEAQRLGAKPLARILGWGHAGVEPRVMGLGPVEAVPIALR 301

Query: 304 RAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALITVKA 363
           RAG+ +  +DVIE+NEAFAAQACAV+  LG DP K N NGSGISLGHP+GATGA+ TVK 
Sbjct: 302 RAGVTLDRIDVIESNEAFAAQACAVSAQLGFDPEKTNVNGSGISLGHPVGATGAINTVKL 361

Query: 364 LHELNRVQGRYALVTMCIGGGQGIAAIFERI 394
           L+EL R  GR  LVTMCIGGGQGIA + ER+
Sbjct: 362 LYELQRSGGRLGLVTMCIGGGQGIALVIERL 392


Lambda     K      H
   0.318    0.134    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: 541
Number of extensions: 19
Number of successful extensions: 2
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: 394
Length of database: 393
Length adjustment: 31
Effective length of query: 363
Effective length of database: 362
Effective search space:   131406
Effective search space used:   131406
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 (21.7 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