GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garK in Cupriavidus basilensis 4G11

Align glycerate 2-kinase (EC 2.7.1.165) (characterized)
to candidate RR42_RS23230 RR42_RS23230 glycerate kinase

Query= metacyc::MONOMER-20837
         (380 letters)



>FitnessBrowser__Cup4G11:RR42_RS23230
          Length = 396

 Score =  272 bits (696), Expect = 1e-77
 Identities = 167/375 (44%), Positives = 215/375 (57%), Gaps = 13/375 (3%)

Query: 3   IIIAPDSFKDSLSAEGVAQAIAAGLSEVWPQAQLIQCPMADGGEGTVDAVLAACKGELRR 62
           I+IAPDSFK SL+A  VA AIAAG+    P A + Q PMADGGEGT+DA+LAA  G+   
Sbjct: 9   IVIAPDSFKGSLAAGQVAAAIAAGIQRALPGATIRQRPMADGGEGTIDAMLAA-GGQRTG 67

Query: 63  QQVRGPLGGTVEARWGWLADSHTAIIEMAEASGL-----QLVPPGQRDACTSTTYGTGEL 117
            +VRG  G    A    LA    A+IE AE  G+        P  QR     +T G G+ 
Sbjct: 68  IEVRGAHGAARIATVALLAGDR-AVIESAEIVGITDPAGMACPVAQR-----STTGLGDA 121

Query: 118 IRAALDLGAERIILAIGGSATNDAGAGAMQALGAQLFDAEAQTLPPGGLALSRLAHISLE 177
           I+A LDLG   I + +GGS+TND GAG +  LG +L DA+ + +PP   AL +LA I   
Sbjct: 122 IKALLDLGVREIFVGLGGSSTNDGGAGLLHGLGLRLLDAQGRDIPPTPAALPQLAAIDAS 181

Query: 178 NLDPRLAQVRFEIAADVNNPLCGPHGASAIFGPQKGASPVHVQQLDAALGHFADHCARVL 237
            LDPRLA  R     DV NPL GP GA+A+FGPQKG     V  +DAAL  +    A  L
Sbjct: 182 QLDPRLASTRLVAMCDVTNPLTGPLGATAVFGPQKGVQAQDVDAIDAALAGYDRLLAPAL 241

Query: 238 PKDVRDEPGSGAAGGLGFAAKAFLGAQFRAGVEVVAELVGLEDAVRGADLVITGEGRFDA 297
            +   D  G+GAAGGLG+A    LGAQ R G ++VA+ V L+ A+ GAD +ITGEGR D 
Sbjct: 242 GRHAVDAAGAGAAGGLGYAL-LMLGAQMRPGADIVADCVDLDGALAGADWLITGEGRSDV 300

Query: 298 QTLRGKTPFGVARIAGQHNVPVIVIAGTLGEGYEQMYAHGVAAAFALPAGPMSLEQACSE 357
           QTL GK P    + A    VP  +++G +               F+L  GP+++EQA + 
Sbjct: 301 QTLSGKAPLIACQRAHACGVPASLLSGAIDPAALPALGTHFTGCFSLAPGPITVEQAMAN 360

Query: 358 APRLLRERASDIARV 372
           A  LL + A  +AR+
Sbjct: 361 ASALLSDAAEQMARL 375


Lambda     K      H
   0.318    0.135    0.398 

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: 448
Number of extensions: 30
Number of successful extensions: 3
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: 380
Length of database: 396
Length adjustment: 30
Effective length of query: 350
Effective length of database: 366
Effective search space:   128100
Effective search space used:   128100
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