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.
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:
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