GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garK in Herbaspirillum seropedicae SmR1

Align glycerate 2-kinase (EC 2.7.1.165) (characterized)
to candidate HSERO_RS10055 HSERO_RS10055 glycerate kinase

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



>FitnessBrowser__HerbieS:HSERO_RS10055
          Length = 387

 Score =  283 bits (723), Expect = 7e-81
 Identities = 160/376 (42%), Positives = 221/376 (58%), Gaps = 3/376 (0%)

Query: 3   IIIAPDSFKDSLSAEGVAQAIAAGLSEVWPQAQLIQCPMADGGEGTVDAVLAACKGELRR 62
           ++IAPDSFK SLSAE VA+AI AG+    P A++   P+ADGGEGT+DA++ A  GE   
Sbjct: 13  VVIAPDSFKGSLSAEDVARAIGAGIQAAIPDAEIRLRPIADGGEGTLDALMHA-GGERFA 71

Query: 63  QQVRGPLGGTVEARWGWLADSHTAIIEMAEASGLQLVPPGQRDACTSTTYGTGELIRAAL 122
              R   G   EA  G L D  +A++E A   GL             +T G G+ I+A L
Sbjct: 72  VACRNAAGQMTEALVGILKDG-SAVVESAAIVGLTDTAGTAVAVERRSTLGVGDAIKALL 130

Query: 123 DLGAERIILAIGGSATNDAGAGAMQALGAQLFDAEAQTLPPGGLALSRLAHISLENLDPR 182
           D GA   ++A+GGS+TND GAG + ALG   +DA    + P    L R+  +    LD R
Sbjct: 131 DRGARSFLVALGGSSTNDGGAGLLAALGVVFYDAAGVEVAPAPAELHRVVRVDASGLDAR 190

Query: 183 LAQVRFEIAADVNNPLCGPHGASAIFGPQKGASPVHVQQLDAALGHFADHCARVLPKDVR 242
           + +  F   +DV+NPLCG  GA+A+FGPQKG  P  V  LD  L HFA      L +   
Sbjct: 191 VKEAHFVAMSDVDNPLCGAEGATAVFGPQKGVQPDQVAPLDQTLAHFAQVLEEALGRQAA 250

Query: 243 DEPGSGAAGGLGFAAKAFLGAQFRAGVEVVAELVGLEDAVRGADLVITGEGRFDAQTLRG 302
             PG+GAAGGLG+A    LGAQFR+G + VA+ +GL+ A+ GAD +ITGEGR DAQTL G
Sbjct: 251 TLPGAGAAGGLGYAL-LMLGAQFRSGAQTVADHIGLDQALTGADWLITGEGRSDAQTLHG 309

Query: 303 KTPFGVARIAGQHNVPVIVIAGTLGEGYEQMYAHGVAAAFALPAGPMSLEQACSEAPRLL 362
           K PF  ++ A Q  VP  +++G +            +  F++  GP +L+ A ++AP+LL
Sbjct: 310 KAPFIASQRARQLGVPATLLSGGIDRHSLAQLQTSFSGCFSIVFGPGALQDAIAQAPQLL 369

Query: 363 RERASDIARVWRLASS 378
           +  A  +AR+W+ A++
Sbjct: 370 QASAEQLARLWQSAAA 385


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: 360
Number of extensions: 19
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: 387
Length adjustment: 30
Effective length of query: 350
Effective length of database: 357
Effective search space:   124950
Effective search space used:   124950
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