GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PRAI in Marinobacter adhaerens HP15

Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate GFF3066 HP15_3010 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase

Query= BRENDA::P16250
         (240 letters)



>FitnessBrowser__Marino:GFF3066
          Length = 245

 Score =  143 bits (360), Expect = 4e-39
 Identities = 83/234 (35%), Positives = 131/234 (55%), Gaps = 4/234 (1%)

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

Query: 64  RALIAEVAQAM-DIKVELSGGIRDDDTLAAALATGCTRVNLGTAALETPEWVAKVIAEHG 122
             ++  +A+   D+ +++ GGIR  +T+ A L  G   V +GT A++ PE+V ++  +  
Sbjct: 63  GEIVQAIARKYPDLPIQIGGGIRSAETIEAYLKAGVQWVIIGTKAVKEPEFVTEMCKKFP 122

Query: 123 DKIAVGLDVRGTTLRGRGWTRDGGDLYETL-DRLNKEGCARYVVTDIAKDGTLQGPNLEL 181
             I VGLD +   +   GW      +   L  R   +G    V TDI++DG +QG N+E 
Sbjct: 123 GHIIVGLDAKDGRVATDGWAEVSEVMATDLAKRFANDGVDAIVYTDISRDGMMQGVNVEA 182

Query: 182 LKNVCAATDRPVVASGGVSSLDDLRAIAGLVPAGVEGAIVGKALYAKAFTLEEA 235
              +      PV+ASGGV+++DDL+ +A +   G+ GAI G+A+Y     + EA
Sbjct: 183 TAALAEEGGIPVIASGGVTNMDDLKRLATVADKGILGAITGRAIYEGTLDVAEA 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: 180
Number of extensions: 14
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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