GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PRAI in Methanosarcina acetivorans C2A

Align N-(5'-phosphoribosyl)anthranilate isomerase 1; PRAI 1; EC 5.3.1.24 (uncharacterized)
to candidate WP_048065580.1 MA_RS15670 N-(5'-phosphoribosyl)anthranilate isomerase

Query= curated2:Q8PT98
         (234 letters)



>NCBI__GCF_000007345.1:WP_048065580.1
          Length = 238

 Score =  362 bits (930), Expect = e-105
 Identities = 183/233 (78%), Positives = 208/233 (89%)

Query: 2   RKRLKTRIKICGMCSPEDMEMAALYGADAVGFITEVPIESPRKLDSDTAASLISKLPECL 61
           + R+KTR+KICG+ SP+D+E AALYGADAVGFITEVP+ESPRKLDSDTAA+LISK+P+CL
Sbjct: 6   KTRIKTRVKICGIRSPKDIEFAALYGADAVGFITEVPVESPRKLDSDTAAALISKVPKCL 65

Query: 62  DSVMVIMPENSSRALELIEKVRPDIVQIHSNLPSVELEVIREKTDIPIIKTLSVPAGMGA 121
           DSVMVIMPE S+ ALELIEKV+P+IVQIHS+LP  EL+ +REK DIPIIKTLSVPA   A
Sbjct: 66  DSVMVIMPETSTSALELIEKVKPNIVQIHSDLPLSELKAVREKADIPIIKTLSVPAEQEA 125

Query: 122 SRVQSPVKRLLDEVRRLEESGVVDSILLDSGIAGKTGGTGYVHDWDLSRRIADETELPLI 181
            ++ + V RLL+EVR LEESG+VDS+LLDSGIAGKTGGTG VHDWDLSRRIA+ETELPLI
Sbjct: 126 PKLHNIVTRLLEEVRELEESGIVDSVLLDSGIAGKTGGTGCVHDWDLSRRIAEETELPLI 185

Query: 182 LAGGLKPENVQEAIRIVSPYAVDAASGVEILGKKDAVKIRSFIEEVRCANAFL 234
           LAGGLKPENVQEAIR VSPYAVD ASGVE  GKKD+VK+R FIEEVRC  AFL
Sbjct: 186 LAGGLKPENVQEAIRSVSPYAVDTASGVETQGKKDSVKVRKFIEEVRCTYAFL 238


Lambda     K      H
   0.317    0.135    0.376 

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: 297
Number of extensions: 7
Number of successful extensions: 1
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: 234
Length of database: 238
Length adjustment: 23
Effective length of query: 211
Effective length of database: 215
Effective search space:    45365
Effective search space used:    45365
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: 41 (21.6 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Jul 25 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