GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PRAI in Thermovibrio ammonificans HB-1

Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_013536927.1 THEAM_RS00875 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase

Query= BRENDA::P16250
         (240 letters)



>NCBI__GCF_000185805.1:WP_013536927.1
          Length = 244

 Score =  165 bits (418), Expect = 7e-46
 Identities = 96/238 (40%), Positives = 137/238 (57%), Gaps = 11/238 (4%)

Query: 6   LLPAVDVRDGQAVRLVHGESGTETSY-GSPLEAALAWQRSGAEWLHLVDLDAAF-GTGDN 63
           ++PAVD++ G+ VRL  G++  E  Y  +P+E A  W+  GA  +H+VDLD AF G   N
Sbjct: 4   VIPAVDIKGGKCVRLYQGKADAEKVYFENPVEVAKRWEEEGASIIHVVDLDGAFEGVPKN 63

Query: 64  RALIAEVAQAMDIKVELSGGIRDDDTLAAALATGCTRVNLGTAALETPEWVAKVIAEHGD 123
             ++ E+ Q + I V+  GG+R    L      G +RV +GT A+E PE   K   E  D
Sbjct: 64  LPIVKEIVQELSIPVQFGGGVRTRKALEELFKAGVSRVVVGTVAVEEPELFKKWTEEFPD 123

Query: 124 KIAVGLDVRGTTLRGRGWTRDGG----DLYETLDRLNKEGCARYVVTDIAKDGTLQGPNL 179
           K+ VG+D +      RGW    G    +L   LD+L   G   +V TDI++DGTL  PN 
Sbjct: 124 KLVVGIDAKNGIATTRGWVELSGIPATELARNLDQLPIWG---FVYTDISRDGTLTSPNF 180

Query: 180 ELLKNVCAATDRPVVASGGVSSLDDLRAIAGLVPAGVEGAIVGKALYAKAFTLEEALE 237
           E ++   +A + PV+ASGGVSS +DL+ ++ +    V GAIVGKALY     L+EA+E
Sbjct: 181 EEVEKFASAVEHPVIASGGVSSPEDLKRLSKI--KNVAGAIVGKALYEGKVNLKEAIE 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: 154
Number of extensions: 10
Number of successful extensions: 5
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: 244
Length adjustment: 23
Effective length of query: 217
Effective length of database: 221
Effective search space:    47957
Effective search space used:    47957
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