GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argE in Sinorhizobium fredii NGR234

Align Predicted argE by GapMind curators (no experimental data)
to candidate WP_012709239.1 NGR_RS24810 M20 aminoacylase family protein

Query= predicted:W3Y6L2
         (394 letters)



>NCBI__GCF_000018545.1:WP_012709239.1
          Length = 387

 Score =  233 bits (595), Expect = 5e-66
 Identities = 131/374 (35%), Positives = 210/374 (56%), Gaps = 9/374 (2%)

Query: 12  ASQYKEQVVAWRRHIHSHPELSGEEKETSAFIQSVLTDLGIP-FKADVYKYAVIGEIKGA 70
           A++ + +V  WRRH+H +PEL    + T+AF++  L + G+      + +  V+G I+G 
Sbjct: 7   AAELQNEVTEWRRHLHMNPELLFAVENTAAFVEKKLREFGVDEIVTGLGRTGVVGLIRGN 66

Query: 71  FD-GPVVGLRADMDALPITEVTGLPFTSENPGVMHACGHDSHMAILLGAAAILQSVKDQL 129
              G  +GLRADMDALPITE +G  ++S  PG MHACGHD H A+LLGAA  L   ++  
Sbjct: 67  LGAGRTIGLRADMDALPITETSGKAWSSTTPGKMHACGHDGHTAMLLGAAKYLAETRN-F 125

Query: 130 HGTVKLVIQPAEEEALIKGAQGIVDSGVLDD--VDEIYGLHVWPQLPVGTVGLKKGNLMA 187
            G V ++ QPAEE     G   +V  G+++   ++E+YG+H  P +PVG  G + G +MA
Sbjct: 126 SGNVAVIFQPAEEGG--GGGNEMVKDGMMERFAIEEVYGMHNMPGMPVGHFGSRVGPIMA 183

Query: 188 ASDRFLVHIKGKATHGAEPHNGIDAIVAAANWIVNVESMVARETNPMDNLVCTIGVFNSG 247
           ++D F + +KG+  H A+PH  ID I   A  +  ++++ +R  +P+ ++V ++  FN+G
Sbjct: 184 STDEFTITVKGRGGHAAQPHKTIDPIAIGAQIVNALQTIASRTVDPLASIVVSVTKFNAG 243

Query: 248 DRYNVGSGDAYLEGTCRTYDPAKRDYIERRLGESLKALDMMFGTTSTLEYRRGHGATIND 307
             +NV    A L GT R   P  RD  E R+ +  +++   +G T  + Y R +  T+N 
Sbjct: 244 FAHNVIPEQAVLAGTVRALTPQVRDTGEARIRQIAESIAGAYGATVDVWYGRNYPVTVNH 303

Query: 308 ADAIDYVTHIVKTYLGKDAVVHPEFPSMAAEDFSAYLNKIKGAFLWLGTGFEGNPALHNA 367
           A    +   +  T  G+  V     P M  EDFS  L    GAF+++G G   +  LH+ 
Sbjct: 304 ATETGHALAVAATVAGEGNVNAALDPMMGGEDFSYMLLARPGAFVFIGNG--ESAGLHHP 361

Query: 368 AFTIDESILEPGIT 381
           A+  ++ ++  GI+
Sbjct: 362 AYDFNDDVIPHGIS 375


Lambda     K      H
   0.318    0.136    0.401 

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: 398
Number of extensions: 13
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: 394
Length of database: 387
Length adjustment: 31
Effective length of query: 363
Effective length of database: 356
Effective search space:   129228
Effective search space used:   129228
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 Jul 25 2024. The underlying query database was built on Jul 25 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