GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PRAI in Enterococcus termitis LMG 8895

Align N-(5'-phosphoribosyl)anthranilate isomerase; PRAI; EC 5.3.1.24 (uncharacterized)
to candidate WP_069663041.1 BCR25_RS07710 phosphoribosylanthranilate isomerase

Query= curated2:C1CT52
         (199 letters)



>NCBI__GCF_001730305.1:WP_069663041.1
          Length = 198

 Score =  171 bits (434), Expect = 6e-48
 Identities = 93/195 (47%), Positives = 128/195 (65%), Gaps = 5/195 (2%)

Query: 3   KVKICGLSTKEAVETAVSAGADYIGFVFAPSKRQVTLEEAAELAKLIPADVKKVGVFVSP 62
           KVKICGL+T+E V+TAV  GADY+GFVFA SKR +  E+  E+ K +P +VKKVGVFV+P
Sbjct: 2   KVKICGLTTREQVDTAVKKGADYLGFVFAESKRAIRPEKVKEITKEVPKNVKKVGVFVTP 61

Query: 63  SRVELLEAIDKVGLDLVQVHGQVAADLFENLPCASIQAVQVDGNGHVPNSQADYLLFDAP 122
           S  E   AI + GLD++Q+HG++    +      +I     +    +  + A+YLLFDA 
Sbjct: 62  SNQEAETAIREAGLDMIQIHGKLVTRSYSVPVIQAIPVGSYEQEKMMKETTAEYLLFDAL 121

Query: 123 ----VAGSGQSFDWGQLDTTGLA-QPFFIAGGLNEDNVVKAIQHFTPYAVDVSSGVETDG 177
               + G+G+ FDW QL+ + L  +  FIAGGL  +NV +A   F+PYAVDVSSGVET+G
Sbjct: 122 PQKFIGGNGKPFDWQQLNISKLKNKKIFIAGGLTSENVQEARATFSPYAVDVSSGVETNG 181

Query: 178 QKDHEKIRRFIERVK 192
            KD  KI  F+++ K
Sbjct: 182 IKDLAKISEFLKKAK 196


Lambda     K      H
   0.317    0.134    0.384 

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: 142
Number of extensions: 4
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: 199
Length of database: 198
Length adjustment: 20
Effective length of query: 179
Effective length of database: 178
Effective search space:    31862
Effective search space used:    31862
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 (21.6 bits)
S2: 45 (21.9 bits)

This GapMind analysis is from Jul 26 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