GapMind for Amino acid biosynthesis

 

Alignments for a candidate for split_metH_2 in Clostridium kluyveri DSM 555

Align Methionine synthase component, methyltransferase domain (EC:2.1.1.13) (characterized)
to candidate WP_012101348.1 CKL_RS04800 homocysteine methyltransferase

Query= reanno::Phaeo:GFF1321
         (338 letters)



>NCBI__GCF_000016505.1:WP_012101348.1
          Length = 801

 Score =  146 bits (368), Expect = 2e-39
 Identities = 92/278 (33%), Positives = 151/278 (54%), Gaps = 10/278 (3%)

Query: 18  DGATGTNLFNMGLQSGDAPELWNVDEPKKITALYQGAVDAGSDLFLTNTFGGTAARLKLH 77
           DGA GT L   GL+ G+ PE+ N+  P+ I+ +++  +DAG+D+  TNTFG  A  LK  
Sbjct: 18  DGAMGTMLQKAGLKLGELPEVLNITNPEIISGIHRKYLDAGADIITTNTFG--ANELKYD 75

Query: 78  DAHRRVRELNVAGAELGRNVADRSERKIAVAGSVGPTGEIMQPVGELSHALAVEMFHEQA 137
            +   + ++  AG +L +  A        VA  +GP G+IM+P G LS   A ++F  Q 
Sbjct: 76  SSDYTIEDVISAGVKLAKQEAGDK----LVALDIGPIGKIMEPTGNLSFESAYKLFKNQI 131

Query: 138 EALKEGGVDVLWLETISAPEEYRAAAEAFK-LADMPWCGTMSFDTAGRTMMGVTSADMAQ 196
              ++ G DV+ +ET++   E +AA  A K  +++P   TM+F   GRT+MG  +  M  
Sbjct: 132 VIGEKSGADVVLIETMTDLYEAKAAVLAAKENSNIPIFCTMTFQEDGRTLMGTDAKTMVF 191

Query: 197 LVEEFDPAPLAFGANCGTGASDILRTVLGFAAQGTTRPIISKGNAGIPKYVDGHIHYDGT 256
           ++E      L  G NC  G  + L+ ++    + ++ P++ + NAG+P+Y   +  YD +
Sbjct: 192 VLEALGVDVL--GVNCSLGPKE-LQGIVEEILKYSSIPVMVQPNAGLPRYDGENTIYDIS 248

Query: 257 PTLMGEYAAMARDCGAKIIGGCCGTMPDHLRAMREALD 294
           P    E        G +++GGCCGT P+ +R  R+ L+
Sbjct: 249 PEDFAENVLTMAQKGIRVLGGCCGTTPEFIRMCRKDLE 286


Lambda     K      H
   0.317    0.134    0.397 

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: 604
Number of extensions: 32
Number of successful extensions: 4
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: 338
Length of database: 801
Length adjustment: 35
Effective length of query: 303
Effective length of database: 766
Effective search space:   232098
Effective search space used:   232098
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: 52 (24.6 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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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