GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garK in Thermithiobacillus tepidarius DSM 3134

Align glycerate 2-kinase (EC 2.7.1.165) (characterized)
to candidate WP_211218710.1 G579_RS0109880 glycerate kinase

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



>NCBI__GCF_000423825.1:WP_211218710.1
          Length = 387

 Score =  343 bits (879), Expect = 6e-99
 Identities = 182/381 (47%), Positives = 245/381 (64%), Gaps = 2/381 (0%)

Query: 1   MKIIIAPDSFKDSLSAEGVAQAIAAGLSEVWPQAQLIQCPMADGGEGTVDAVLAACKGEL 60
           ++++IAPD+FK SL A  VA+AIAAG     P A +   P+ADGGEGTV ++LAA  G L
Sbjct: 8   LQLVIAPDAFKGSLEARAVAEAIAAGCRRALPDAVIRCFPLADGGEGTVASLLAARGGRL 67

Query: 61  RRQQVRGPLGGTVEARWGWLADSHTAIIEMAEASGLQLVPPGQRDACTSTTYGTGELIRA 120
           R  +V GPLG  VEA +  L D   A+IE+A ASGL L+P  +RD   ++++GTGEL+R 
Sbjct: 68  RGVRVHGPLGEPVEAGYAILPDG-AAVIELAAASGLPLLPAARRDPLRASSFGTGELVRD 126

Query: 121 ALDLGAERIILAIGGSATNDAGAGAMQALGAQLFDAEAQTLPPGGLALSRLAHISLENLD 180
           ALD G  R+I+ +GGSA ND G G +QALG +  DA+ Q++ PGG AL  +A I +   D
Sbjct: 127 ALDQGCRRLIVGLGGSAVNDGGLGLLQALGFRFLDAKGQSVGPGGGALGAIARIDVSQAD 186

Query: 181 PRLAQVRFEIAADVNNPLCGPHGASAIFGPQKGASPVHVQQLDAALGHFADHCARVLPKD 240
           PRL   +   A DV+ PL GP GA+  FGPQKGA+P  ++ L+A + H+AD  A  L   
Sbjct: 187 PRLRDAQLIAATDVDTPLLGPEGATHTFGPQKGATPAMLETLEAGMRHYADKIAETLAVR 246

Query: 241 VRDEPGSGAAGGLGFAAKAFLGAQFRAGVEVVAELVGLEDAVRGADLVITGEGRFDAQTL 300
           V D PG+GAAGG G A  AFLGA+ R+GV +V E +G+  A+ GADL+ITGEGR D QT 
Sbjct: 247 VHDLPGAGAAGGCGAALHAFLGAEIRSGVALVMEALGVAAALAGADLLITGEGRIDGQTR 306

Query: 301 RGKTPFGVARIAGQHNVPVIVIAGTLGEGYEQMYAHGVA-AAFALPAGPMSLEQACSEAP 359
           RGK P+GVAR+A +H VPV+++AG +      +   G+      +P  PMSLE A +   
Sbjct: 307 RGKAPYGVARLAKRHGVPVLMLAGAVAPEARMLLEDGICDVLLGIPPAPMSLEIALAHTA 366

Query: 360 RLLRERASDIARVWRLASSKG 380
           + L + A  + R +RL    G
Sbjct: 367 QHLADGAEQLLRAYRLGRRSG 387


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: 453
Number of extensions: 17
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 Apr 09 2024. 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