GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PRAI in Epibacterium ulvae U95

Align N-(5'-phosphoribosyl)anthranilate isomerase 2; PRAI 2; EC 5.3.1.24 (uncharacterized)
to candidate WP_090218246.1 CV091_RS10410 phosphoribosylanthranilate isomerase

Query= curated2:Q8PRX4
         (226 letters)



>NCBI__GCF_002796795.1:WP_090218246.1
          Length = 229

 Score =  111 bits (278), Expect = 1e-29
 Identities = 69/226 (30%), Positives = 121/226 (53%), Gaps = 4/226 (1%)

Query: 3   IKVCGIKRVEDAVMAAYCGADAIGLVVGRKHNSDDFIDKHLAQKIVRECPPYISPVLVTE 62
           ++V GI   ++A +    GAD IG  +      DD I +  A+ I++        VL++ 
Sbjct: 5   VQVAGIIDSKEAELCFANGADWIGFPLRLPSGKDD-ISEADAKAIIKTLKAPQRAVLISY 63

Query: 63  LDDAEEISGLVHETGVTSVQLHSDCTVDSIISLRKTFPNIKIIKNFHVIG---PGVIHAM 119
           +  A E+S    E G+ +VQLH D +++ +  LR+  P++ ++K+  V     P +   +
Sbjct: 64  MTTAAEVSQFCDELGLDAVQLHGDISMEELAKLRQMRPDLYLLKSLVVSADNLPALRQLI 123

Query: 120 KPFESVVDAFILDTLDLANDKVGSTGLVHDWSISRKIVKEVSRPVILAGGLTPENVGEAI 179
                 +D +I DT D      G+TG+ HDW++S ++V+   +P+++AGGL+P+NV +AI
Sbjct: 124 DDSAEYIDMYITDTFDPKTGAKGATGMTHDWNVSAELVRHSPKPLMMAGGLSPDNVYDAI 183

Query: 180 RVVNPYGVDASSGLKDSNGFKDEMKVINFVHRAKNDFFKVRNLSLE 225
             V P  VDA S L+ ++  K   K+  F   AK  F ++  L+ +
Sbjct: 184 MQVRPAAVDAHSLLEGTDKRKSAEKMRVFSAEAKRAFSEMSVLAAQ 229


Lambda     K      H
   0.320    0.138    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: 121
Number of extensions: 7
Number of successful extensions: 2
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: 226
Length of database: 229
Length adjustment: 22
Effective length of query: 204
Effective length of database: 207
Effective search space:    42228
Effective search space used:    42228
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 (21.8 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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