GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Sphingomonas koreensis DSMZ 15582

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate Ga0059261_0982 Ga0059261_0982 acetyl-CoA acetyltransferases

Query= SwissProt::P07097
         (392 letters)



>FitnessBrowser__Korea:Ga0059261_0982
          Length = 390

 Score =  549 bits (1414), Expect = e-161
 Identities = 272/388 (70%), Positives = 317/388 (81%)

Query: 3   TPSIVIASARTAVGSFNGAFANTPAHELGATVISAVLERAGVAAGEVNEVILGQVLPAGE 62
           T  ++ A+ RT VGSF GAFA+TPAHELG   I A LE+A V   EV+EVILGQVL A +
Sbjct: 2   TEVVITAAKRTPVGSFLGAFASTPAHELGRIAIEAALEQAEVKGEEVSEVILGQVLTAAQ 61

Query: 63  GQNPARQAAMKAGVPQEATAWGMNQLCGSGLRAVALGMQQIATGDASIIVAGGMESMSMA 122
           GQNPARQA+M AGVP+E  AWG+NQ+CGSGLRAVAL  Q + TGDA+I+VAGG ESMS+A
Sbjct: 62  GQNPARQASMAAGVPKEVPAWGLNQVCGSGLRAVALAAQAVQTGDATIVVAGGQESMSLA 121

Query: 123 PHCAHLAGGVKMGDFKMIDTMIKDGLTDAFYGYHMGTTAENVAKQWQLSRDEQDAFAVAS 182
            H   L  G KMGD  +IDTMIKDGLTD F GYHMG TAEN+A+Q+Q++R EQD FAV S
Sbjct: 122 AHAQSLRAGAKMGDVGLIDTMIKDGLTDVFNGYHMGITAENLAEQYQVTRGEQDEFAVRS 181

Query: 183 QNKAEAAQKDGRFKDEIVPFIVKGRKGDITVDADEYIRHGATLDSMAKLRPAFDKEGTVT 242
           QN AEAA+ +GRFKDEI P  +KGRKGD  VD DEYIR GATLDS+A LRPAF K+GTVT
Sbjct: 182 QNLAEAARSEGRFKDEIAPVTIKGRKGDTVVDQDEYIRAGATLDSVAGLRPAFKKDGTVT 241

Query: 243 AGNASGLNDGAAAALLMSEAEASRRGIQPLGRIVSWATVGVDPKVMGTGPIPASRKALER 302
           AGNASGLNDGAAA ++MS  EA +RG   L  I SWAT GVDP +MG GP+PAS+KALE+
Sbjct: 242 AGNASGLNDGAAALVVMSREEADKRGATVLATIKSWATAGVDPSIMGIGPVPASKKALEK 301

Query: 303 AGWKIGDLDLVEANEAFAAQACAVNKDLGWDPSIVNVNGGAIAIGHPIGASGARILNTLL 362
           AGW + DLDL+EANEAFAAQA +V K+LG+DP+ VNVNGGAIAIGHPIGASGAR+L TLL
Sbjct: 302 AGWTVADLDLIEANEAFAAQALSVGKELGFDPNKVNVNGGAIAIGHPIGASGARVLTTLL 361

Query: 363 FEMKRRGARKGLATLCIGGGMGVAMCIE 390
           +EM+RR A+KGLATLCIGGGMG+AMC+E
Sbjct: 362 YEMQRRDAKKGLATLCIGGGMGIAMCVE 389


Lambda     K      H
   0.317    0.132    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: 496
Number of extensions: 13
Number of successful extensions: 1
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: 392
Length of database: 390
Length adjustment: 31
Effective length of query: 361
Effective length of database: 359
Effective search space:   129599
Effective search space used:   129599
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