Align phosphoribosylanthranilate isomerase; EC 5.3.1.24 (characterized)
to candidate WP_057687224.1 ABB28_RS15210 phosphoribosylanthranilate isomerase
Query= CharProtDB::CH_021917 (235 letters) >NCBI__GCF_001431535.1:WP_057687224.1 Length = 218 Score = 150 bits (379), Expect = 2e-41 Identities = 91/214 (42%), Positives = 121/214 (56%), Gaps = 8/214 (3%) Query: 21 RTRIKLCGLSRPDDVLHAAALGADAIGLVFYAKSPRAVTIAQAAELARLAPPFVSVVGLF 80 RTRIK CG++R DV A LG DA+G +F +S R V A+A + + P V VV LF Sbjct: 7 RTRIKFCGMTRAGDVRLAGELGVDAVGFIFARESKRRVAPAEARAMRQAIAPMVDVVALF 66 Query: 81 VNATAAEIEAVVRDVPLTLLQFHGDETPEQCDALGRAARLPWVRAVRVGPSTQSADLVES 140 + T E+ V+R V TLLQFHGDE C R +P+++A+ +G + + Sbjct: 67 RDNTREEVREVLRTVRPTLLQFHGDEDEGFC----RGFNMPYLKAIAMG-GREEVNARTL 121 Query: 141 SLHYSKARGLLFDTLVP-DYGGSGKVFDWSLIPAELARRAVLSGGLNAQNVGDAIRQLRP 199 L Y A G LFD+ P GG+G FDW+ IP+ L R +L+GGL +N+ DA P Sbjct: 122 QLRYPSAAGFLFDSHAPGGGGGTGVAFDWTRIPSGLHRPFLLAGGLTPENIFDAAVATLP 181 Query: 200 FAVDVSSGIEVEGAKGVKDHARMAAFVRAVRDAD 233 + VDVSSGIE E G+KD M FV +R AD Sbjct: 182 WGVDVSSGIESE--PGIKDGYLMRKFVEEIRRAD 213 Lambda K H 0.319 0.134 0.384 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: 125 Number of extensions: 7 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: 235 Length of database: 218 Length adjustment: 22 Effective length of query: 213 Effective length of database: 196 Effective search space: 41748 Effective search space used: 41748 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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