GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisI in Streptacidiphilus oryzae TH49

Align phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) (characterized)
to candidate WP_037579958.1 BS73_RS17085 MazG family protein

Query= metacyc::MONOMER-21148
         (267 letters)



>NCBI__GCF_000744815.1:WP_037579958.1
          Length = 353

 Score =  125 bits (313), Expect = 2e-33
 Identities = 76/232 (32%), Positives = 113/232 (48%), Gaps = 23/232 (9%)

Query: 6   ASLARLTDVIDRLLAPEGCPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVREEMGDV 65
           A L  L  V+DRL +P GCPWD +QT ESL  YLVEE +ELVEAI  G+   +REE+GDV
Sbjct: 129 ARLLDLVSVMDRLRSPGGCPWDAQQTHESLVKYLVEESYELVEAIEEGDRPALREELGDV 188

Query: 66  MFLLAFLGRLYAD--KGAFTLDDAMANNAAKMIRRHPHVFSDTTYADRDEFLRNWESIKR 123
           +  + F  R+  +  +  F +D+       K++ RHPHVF+D      +     W+ +K 
Sbjct: 189 LLQVLFHSRIAQEHPEDPFGIDEVAGGIVDKLVFRHPHVFADAGVPASEHLEATWDKLKA 248

Query: 124 AEKADAEGEPQGVYDSLPASLPPLLKAYRIHSKAARVGFTWPEDEDVERQVEAEWLELLD 183
           AEK     + + + D +P   P L  A ++ S+A + G   P + +   Q          
Sbjct: 249 AEK-----QRESLTDGVPLGQPSLALAAKLLSRARKAGLDLPLETEFTPQA--------- 294

Query: 184 VLAGDDKAAQENELGDLIFSLVELGRRKGIKANTALDMTNLKFLRRFRRMEA 235
                     E +LG+L+ +L +      I    AL    L++  R R  EA
Sbjct: 295 -------PPAEEDLGELLLALAKTADAHSIDPEQALRAAALRYRARIREAEA 339


Lambda     K      H
   0.318    0.134    0.393 

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: 237
Number of extensions: 10
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: 267
Length of database: 353
Length adjustment: 27
Effective length of query: 240
Effective length of database: 326
Effective search space:    78240
Effective search space used:    78240
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: 48 (23.1 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