GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisI in Streptacidiphilus oryzae TH49

Align Phosphoribosyl-ATP pyrophosphatase; PRA-PH; EC 3.6.1.31 (uncharacterized)
to candidate WP_037568880.1 BS73_RS02710 LacI family transcriptional regulator

Query= curated2:C5CBJ9
         (87 letters)



>NCBI__GCF_000744815.1:WP_037568880.1
          Length = 334

 Score = 32.7 bits (73), Expect = 3e-06
 Identities = 28/92 (30%), Positives = 46/92 (50%), Gaps = 11/92 (11%)

Query: 3   TFDELYAELTRKVQERPEGSGTVAQIDAGVHAI-------GKKVVEEAAEVWMAAEYESD 55
           TF+     LTR ++ERPE SG V Q +A +  +       G+ V E+A+ V +  E  + 
Sbjct: 222 TFESTAGVLTRILEERPETSGFVVQNEAAIRPLLTLLRQFGRVVPEDASVVAICPESVAL 281

Query: 56  EAAAEEISQLLYHVQTMMIARGISLEDVYRHL 87
           +++ +  S     +    + RG +LE V  HL
Sbjct: 282 QSSPQLTS---VSIPAERMGRG-ALELVMAHL 309


Lambda     K      H
   0.314    0.128    0.348 

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: 48
Number of extensions: 1
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: 87
Length of database: 334
Length adjustment: 18
Effective length of query: 69
Effective length of database: 316
Effective search space:    21804
Effective search space used:    21804
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 43 (21.2 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