GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PRAI in Enterococcus termitis LMG 8895

Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_069661634.1 BCR25_RS00405 imidazole glycerol phosphate synthase subunit HisF

Query= BRENDA::P16250
         (240 letters)



>NCBI__GCF_001730305.1:WP_069661634.1
          Length = 251

 Score = 86.7 bits (213), Expect = 4e-22
 Identities = 64/210 (30%), Positives = 108/210 (51%), Gaps = 15/210 (7%)

Query: 6   LLPAVDVRDGQAVRLVHGESGTETSYGSPLEAALAWQRSGAEWLHLVDLDAAFGTGDNRA 65
           ++P +DV DG+ V+ V+  +  +   G P++ A A+   GA+ L  +D+ A   T D R 
Sbjct: 6   IIPCLDVTDGRVVKGVNFVNLQDV--GDPVDIARAYNEQGADELVFLDITA---TSDERQ 60

Query: 66  LIAEV----AQAMDIKVELSGGIRDDDTLAAALATGCTRVNLGTAALETPEWVAKVIAEH 121
            + +V    A  + I + + GGIR  D +   L  G  +++L +AA++ PE +     + 
Sbjct: 61  TMVDVVTRTAAEVFIPLTVGGGIRCIDDMRKLLQAGADKISLNSAAIKQPELIQAGAEKF 120

Query: 122 GDK-IAVGLDVRGTT----LRGRGWTRDGG-DLYETLDRLNKEGCARYVVTDIAKDGTLQ 175
           G + + V +D + +     +  +G   D G D  E   +    G    ++T +  DGT  
Sbjct: 121 GSQCMVVAIDAKRSGDSWHVFVKGGREDTGLDAIEWAKKAVSLGAGEILLTSMDADGTKN 180

Query: 176 GPNLELLKNVCAATDRPVVASGGVSSLDDL 205
           G +LEL + VCAA + PV+ASGG  S DD+
Sbjct: 181 GYDLELNQAVCAAVNVPVIASGGCGSADDI 210



 Score = 30.0 bits (66), Expect = 4e-05
 Identities = 15/66 (22%), Positives = 29/66 (43%)

Query: 143 RDGGDLYETLDRLNKEGCARYVVTDIAKDGTLQGPNLELLKNVCAATDRPVVASGGVSSL 202
           +D GD  +     N++G    V  DI      +   ++++    A    P+   GG+  +
Sbjct: 27  QDVGDPVDIARAYNEQGADELVFLDITATSDERQTMVDVVTRTAAEVFIPLTVGGGIRCI 86

Query: 203 DDLRAI 208
           DD+R +
Sbjct: 87  DDMRKL 92


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: 151
Number of extensions: 14
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 240
Length of database: 251
Length adjustment: 24
Effective length of query: 216
Effective length of database: 227
Effective search space:    49032
Effective search space used:    49032
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.

Links

Downloads

Related tools

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