GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroG in Shewanella oneidensis MR-1

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate 200542 SO1367 chorismate mutase/prephenate dehydratase (NCBI ptt file)

Query= BRENDA::Q9YEJ7
         (270 letters)



>FitnessBrowser__MR1:200542
          Length = 671

 Score = 78.2 bits (191), Expect = 4e-19
 Identities = 56/172 (32%), Positives = 92/172 (53%), Gaps = 17/172 (9%)

Query: 77  FQGLGLEGLKLLRRAGDEAGLPVVTEVLDPRHVETV------------SRYADMLQIGAR 124
           FQ + LEG + L  A  EA +P + + L    +  V            + +ADML +  +
Sbjct: 479 FQAVILEGCQQL--ASKEAIIPKLRQTLHQYDLLCVIAIEQAADMPLATEHADMLFLTGK 536

Query: 125 NMQNFPLLREVGRSGKPVLLKRGFGNTVEELLAAAEYILLEGNWQVVLVERGIRTFEPST 184
            M N  LL + G    P+ L+R    + EE LAA E IL +GN Q++L + GIRT+  + 
Sbjct: 537 QMFNQALLTQAGTLPIPLFLERNDMASYEEFLAATETILSQGNQQLILCDSGIRTYNNAN 596

Query: 185 RFTLDVAAVAVLKEATHLPVIVDPSHPAGRRSLVPALAKAGL-AAGADGLIV 235
             TLD+A++ ++K  +HLP++++P +     +LV  L   G+    ADG+++
Sbjct: 597 LPTLDLASLILIKANSHLPIVINPCYAINEDALV--LQTQGIKQLKADGIVL 646


Lambda     K      H
   0.318    0.136    0.392 

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: 262
Number of extensions: 4
Number of successful extensions: 1
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: 270
Length of database: 671
Length adjustment: 32
Effective length of query: 238
Effective length of database: 639
Effective search space:   152082
Effective search space used:   152082
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 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