GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garK in Burkholderia phytofirmans PsJN

Align glycerate 2-kinase (EC 2.7.1.165) (characterized)
to candidate BPHYT_RS09440 BPHYT_RS09440 glycerate kinase

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



>FitnessBrowser__BFirm:BPHYT_RS09440
          Length = 381

 Score =  301 bits (770), Expect = 3e-86
 Identities = 179/371 (48%), Positives = 224/371 (60%), Gaps = 5/371 (1%)

Query: 3   IIIAPDSFKDSLSAEGVAQAIAAGLSEVWPQAQLIQCPMADGGEGTVDAVLAACKGELRR 62
           ++IAPDSFK SLSAE VAQAIAAG+    P A++  CPMADGGEGT+DA+L    GE R 
Sbjct: 10  VVIAPDSFKGSLSAEQVAQAIAAGIKRARPAAEVRICPMADGGEGTLDAMLTR-GGERRT 68

Query: 63  QQVRGPLGGTVEARWGWLADSHTAIIEMAEASGLQLVPPGQRDACTS-TTYGTGELIRAA 121
             VRG  G   EA  G LAD  +AIIE AE  G+   P G      + +T G GE IRA 
Sbjct: 69  LSVRGAAGPVREALTGLLADG-SAIIETAEVVGIT-DPVGMGVPVEARSTRGMGEAIRAL 126

Query: 122 LDLGAERIILAIGGSATNDAGAGAMQALGAQLFDAEAQTLPPGGLALSRLAHISLENLDP 181
           +D G  R  +A+GGS+TND GAG +  LG +LFDA+   L      L+RLA + +  LD 
Sbjct: 127 MDAGVRRFFVALGGSSTNDGGAGLLAGLGLKLFDAQDNELDATPEQLARLARVDVSQLDA 186

Query: 182 RLAQVRFEIAADVNNPLCGPHGASAIFGPQKGASPVHVQQLDAALGHFADHCARVLPKDV 241
           RL+  +F   +DV+NPL G HGA+A+FGPQKG  P  V  LDAAL  FAD     L +  
Sbjct: 187 RLSSTQFVGMSDVDNPLTGEHGATAVFGPQKGVKPEQVATLDAALARFADLLEPALGRTA 246

Query: 242 RDEPGSGAAGGLGFAAKAFLGAQFRAGVEVVAELVGLEDAVRGADLVITGEGRFDAQTLR 301
           R  PG+GAAGGLGFA    LGAQF  G E VA  +GL+ A+ GAD +ITGEGR D QTL 
Sbjct: 247 RQLPGAGAAGGLGFALH-MLGAQFEPGAETVARQIGLDAALEGADWLITGEGRSDVQTLH 305

Query: 302 GKTPFGVARIAGQHNVPVIVIAGTLGEGYEQMYAHGVAAAFALPAGPMSLEQACSEAPRL 361
           GK PF   R A    VP  +++G +        A   +  F+   GP++LE A  +A RL
Sbjct: 306 GKAPFIACRHAQAAGVPATLLSGGVDSAALPRLAEYFSGCFSPAPGPITLEVAIRDAARL 365

Query: 362 LRERASDIARV 372
           L + A  + R+
Sbjct: 366 LADEAEQLTRL 376


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: 389
Number of extensions: 22
Number of successful extensions: 5
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: 381
Length adjustment: 30
Effective length of query: 350
Effective length of database: 351
Effective search space:   122850
Effective search space used:   122850
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