GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PRAI in Thiomicrospira microaerophila ASL8-2

Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_044413789.1 NA59_RS13115 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase

Query= BRENDA::P16250
         (240 letters)



>NCBI__GCF_000934765.1:WP_044413789.1
          Length = 250

 Score =  143 bits (361), Expect = 3e-39
 Identities = 93/246 (37%), Positives = 135/246 (54%), Gaps = 14/246 (5%)

Query: 6   LLPAVDVRDGQAVRLVHGESGTETSYGSPLEA-ALAWQRSGAEWLHLVDLDAAF-GTGDN 63
           L+PA+D++DGQ VRL  G     T + S + A A  W   GA  LH+VDL+ AF G   N
Sbjct: 3   LIPAIDLKDGQCVRLRQGLMDDATVFSSDIVAMAERWVNQGARRLHMVDLNGAFEGKPVN 62

Query: 64  RALIAEVAQAM-DIKVELSGGIRDDDTLAAALATGCTRVNLGTAALETPEWVAKVIAEHG 122
              + +V +A  D+ +++ GGIRD  T+ A L+ G +   +GT A+  PE+VA+      
Sbjct: 63  GDAVYQVRKAYPDLPIQIGGGIRDLATIEAYLSAGVSYCIIGTKAVHNPEFVAQACKAFP 122

Query: 123 DKIAVGLDVRGTTLRGRGWTRDGGDLYETLD-RLNKEGCARYVVTDIAKDGTLQGPNLEL 181
             I VGLD +   +   GW      L   L  R   +G    + TDI +DG +QG N+E 
Sbjct: 123 GHIMVGLDAKDGYVAINGWAEVTDHLVTELGKRFEDDGVEAIIYTDIGRDGMMQGVNIEA 182

Query: 182 LKNVCAATDRPVVASGGVSSLDDLRAIAGLVPAGVEGAIVGKALY----------AKAFT 231
            + +  A   PVVASGG+++L+D++A+A +   GV GAI G+A+Y          A A T
Sbjct: 183 TQALARALRIPVVASGGITNLEDIKALAKIERDGVVGAITGRAIYEGTLNLAEGQALADT 242

Query: 232 LEEALE 237
           L +ALE
Sbjct: 243 LSQALE 248


Lambda     K      H
   0.315    0.133    0.385 

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: 176
Number of extensions: 16
Number of successful extensions: 4
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: 240
Length of database: 250
Length adjustment: 24
Effective length of query: 216
Effective length of database: 226
Effective search space:    48816
Effective search space used:    48816
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: 42 (22.0 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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