GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aro-dehydratase in Phaeobacter inhibens BS107

Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate GFF2973 PGA1_c30200 prephenate dehydratase

Query= BRENDA::Q9SA96
         (392 letters)



>FitnessBrowser__Phaeo:GFF2973
          Length = 277

 Score =  166 bits (419), Expect = 1e-45
 Identities = 107/282 (37%), Positives = 146/282 (51%), Gaps = 15/282 (5%)

Query: 107 RISFQGIPGAYSETAALKAFPNCETVPCEQFEAAFQAVELWLVDKAVLPIENSVGGSIHR 166
           RI+ QG  G+YS  A  K  P+ + +PC  FE A  AV     + A+LP+ENS  G +  
Sbjct: 4   RIAIQGELGSYSHEACRKERPDMDVLPCRNFEDAINAVRSGAAELAMLPVENSTYGRVAD 63

Query: 167 NYDLLLRHRLHIVQEVHLPVNHCLLGVPGVKKEDIKCVLSHPQALDQCVNSLNNLGIQRI 226
            + LL    LHI+ E  + V+  LLGVPG + EDIK   SH   L QC   L+   I   
Sbjct: 64  IHRLLPHSGLHIIDEAFVRVHINLLGVPGAQLEDIKEAHSHLVLLPQCARFLSENNIHGR 123

Query: 227 SAKDTATAAQTVSSSGKIDVGAIASVRAANIYGLDILAENIQDDVNNVTRFLILAREPMI 286
            + D A AA+ V+  G     A+AS  A  IYGL++LA +I+D  NN TRFL ++R+P  
Sbjct: 124 VSPDNARAARDVAEQGDKSHAALASELAGEIYGLEVLARHIEDHGNNTTRFLTMSRDPNT 183

Query: 287 PRT-DRPYKTSIVFSLEEGPGVLFKALAVFALRSINLSKIESRPQRRRPLRVVDGSNNGS 345
            R  +    TS VF +   P  L+KA+  FA   IN++K+ES         +VDGS   +
Sbjct: 184 ERRGNHGMITSFVFQVRNIPAALYKAMGGFATNGINMTKLES--------YMVDGSFTAT 235

Query: 346 AKYFDYLFYIDFEASMADTRAQHALGHLQEFASFIRILGCYP 387
                  FY D +    D   + A+  L  F + I ILG YP
Sbjct: 236 Q------FYADIDGHPDDPNVRLAMDELAYFTTNIEILGVYP 271


Lambda     K      H
   0.321    0.135    0.402 

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: 250
Number of extensions: 18
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: 392
Length of database: 277
Length adjustment: 28
Effective length of query: 364
Effective length of database: 249
Effective search space:    90636
Effective search space used:    90636
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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