GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PRAI in Salinicoccus carnicancri Crm

Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_017550016.1 C792_RS0113615 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase

Query= BRENDA::P16250
         (240 letters)



>NCBI__GCF_000330705.1:WP_017550016.1
          Length = 233

 Score =  105 bits (263), Expect = 6e-28
 Identities = 70/231 (30%), Positives = 115/231 (49%), Gaps = 7/231 (3%)

Query: 4   LELLPAVDVRDGQAVRLVHGESGTETSYGSPLEAALAWQRSGAEW--LHLVDLDAAFGTG 61
           + ++PA+D+ DG+ VRL  G+    T+     E A+ +     +   +H+VDL  A    
Sbjct: 1   MNIIPAIDIIDGRNVRLKQGDYDQRTAMKRTPEEAIRFYSGFRQVGRIHIVDLMGALKQD 60

Query: 62  DNRALIAEVAQAM-DIKVELSGGIRDDDTLAAALATGCTRVNLGTAALETPEWVAKVIAE 120
              + + E  ++  D+ +++ GG+R+ +T+      G     LGT A+   +W+ + + E
Sbjct: 61  AQESTVIEKLKSQTDLPLQIGGGLRNMETIRQYDRIGIDYFILGTKAILDTDWLKEAVRE 120

Query: 121 HGDKIAVGLDVRGTTLRGRGWTRDGG-DLYETLDRLNKEGCARYVVTDIAKDGTLQGPNL 179
              +I VG D R   +   GWT +    + E +  +     A  + TDI KDG  QGPN 
Sbjct: 121 FPGRIFVGTDARENDIYVNGWTENSDITIDEYIREIEGLDIAGIIYTDINKDGMNQGPNF 180

Query: 180 ELLKNVCAATDRPVVASGGVSSLDDLRAIAGLVPAGVEGAIVGKALYAKAF 230
           E  + +   T   V+ASGGV + +DL  +  L   GV  AIVGKA +  +F
Sbjct: 181 ENTRRINELTRHKVIASGGVRNKEDLDKLGAL---GVRDAIVGKASHNDSF 228


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: 135
Number of extensions: 13
Number of successful extensions: 3
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: 233
Length adjustment: 23
Effective length of query: 217
Effective length of database: 210
Effective search space:    45570
Effective search space used:    45570
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 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