GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Echinicola vietnamensis KMM 6221, DSM 17526

Align P-protein; EC 4.2.1.51; EC 5.4.99.5 (characterized)
to candidate Echvi_0123 Echvi_0123 Prephenate dehydratase

Query= CharProtDB::CH_024084
         (386 letters)



>FitnessBrowser__Cola:Echvi_0123
          Length = 279

 Score =  137 bits (346), Expect = 3e-37
 Identities = 86/281 (30%), Positives = 139/281 (49%), Gaps = 16/281 (5%)

Query: 101 PHSARIAFLGPKGSYSHLAARQYAARHFEQFIES-GCAKFADIFNQVETGQADYAVVPIE 159
           PH  ++A  G KGSY +    Q A   F Q I    C  F+D+   + +  AD  V+ +E
Sbjct: 5   PHQQKVAIQGIKGSYHY----QVALNQFGQDIHVIECLTFSDLVKSITSNDADIGVLALE 60

Query: 160 NTSSGAINDVYDLLQHTSLSIVGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSKF 219
           N+ +GAI   YDL+   +L ++GE  L I H L+V     +  I  V SHP    QC  F
Sbjct: 61  NSIAGAILPNYDLMDRNNLQVIGEFYLPISHQLMVLKGQSIDDITEVRSHPMALLQCKAF 120

Query: 220 LNRYPHWKIEYTESTSAAMEKVAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFTR 279
             +YP  K+     T++  +++++     V A+  ++    YGL +L       + N TR
Sbjct: 121 FEQYPQIKLIEDLDTASVAKEISEQHLQGVGAIAGKSAAEFYGLDILASDIQTIKNNITR 180

Query: 280 FVVLARKAINVSDQVPA----KTTLLMATGQQAGALVEALLVLRNHNLIMTRLESRPIHG 335
           F ++     N +D  P     K ++ +    + G+L + L  +  + L +T+++S P+  
Sbjct: 181 FCIVK----NAADAKPVIGFDKASIKVTIKNEQGSLAKVLTTMSAYRLDLTKIQSLPVID 236

Query: 336 NPWEEMFYLDIQ-ANLESAEMQKALKELGEITRSMKVLGCY 375
            PW   F++D+   NLE  + Q+ALKEL      +KVLG Y
Sbjct: 237 QPWHYAFFIDLLFENLE--DYQQALKELKANGHQIKVLGEY 275


Lambda     K      H
   0.318    0.132    0.374 

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: 210
Number of extensions: 12
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: 386
Length of database: 279
Length adjustment: 28
Effective length of query: 358
Effective length of database: 251
Effective search space:    89858
Effective search space used:    89858
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 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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