GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PRAI in Pseudomonas fluorescens GW456-L13

Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate PfGW456L13_359 Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (EC 5.3.1.16)

Query= BRENDA::P16250
         (240 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_359
          Length = 245

 Score =  132 bits (332), Expect = 6e-36
 Identities = 78/234 (33%), Positives = 124/234 (52%), Gaps = 4/234 (1%)

Query: 6   LLPAVDVRDGQAVRLVHGESGTETSYGS-PLEAALAWQRSGAEWLHLVDLDAAF-GTGDN 63
           ++PA+D++DG  VRL  G     T +   P+  A  W   G   LHLVDL+ AF G   N
Sbjct: 3   IIPAIDLKDGACVRLRQGRMEDSTVFSDDPVSMAAKWVEGGCRRLHLVDLNGAFEGQPVN 62

Query: 64  RALIAEVAQAM-DIKVELSGGIRDDDTLAAALATGCTRVNLGTAALETPEWVAKVIAEHG 122
             ++  +A+   ++ +++ GGIR  +T+   +  G + V +GT A++ P +VA+      
Sbjct: 63  GEVVTAIAKRYPNLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKDPAFVAEACRAFP 122

Query: 123 DKIAVGLDVRGTTLRGRGWTRDGG-DLYETLDRLNKEGCARYVVTDIAKDGTLQGPNLEL 181
            KI VGLD +   +   GW       + +   +   +G +  V TDIAKDG +QG N+  
Sbjct: 123 GKIIVGLDAKDGFVATDGWAEISTIQVIDLAKQFEADGVSSIVYTDIAKDGMMQGCNVPF 182

Query: 182 LKNVCAATDRPVVASGGVSSLDDLRAIAGLVPAGVEGAIVGKALYAKAFTLEEA 235
              + AAT  PV+ASGG+ +L D++ +      G+ GAI G+A+Y     + EA
Sbjct: 183 TAALAAATKIPVIASGGIHNLGDIKTLLDAKAPGIIGAITGRAIYEGTLDVAEA 236


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: 172
Number of extensions: 12
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: 245
Length adjustment: 23
Effective length of query: 217
Effective length of database: 222
Effective search space:    48174
Effective search space used:    48174
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 09 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