Align N-(5'-phosphoribosyl)anthranilate isomerase; Short=PRAI; EC 5.3.1.24 (characterized, see rationale)
to candidate WP_106714835.1 CU100_RS01745 phosphoribosylanthranilate isomerase
Query= uniprot:TRPF_RHIME (215 letters) >NCBI__GCF_003010935.1:WP_106714835.1 Length = 219 Score = 289 bits (739), Expect = 3e-83 Identities = 143/209 (68%), Positives = 172/209 (82%) Query: 1 MKTEVKICGLKTAEAVERAVALGASHVGFIFFPKSPRNIEPDDAGRLAARARGRAKIVAV 60 M ++KICGLKTAE V A+ GA+H+GFIFFPKSPRNI+P AG L A+GRAK VAV Sbjct: 1 MSLDIKICGLKTAETVAAALDGGATHIGFIFFPKSPRNIDPALAGYLRRAAKGRAKAVAV 60 Query: 61 TVDADNDGLDEIVSALDPDVLQLHGSETPERVLSIKALYGLPVMKALAVREASDLERIDP 120 TVDAD+ LD IV+A+ PD+LQLHG E+ RVL IKA YGLPV+KAL++R+ +DL++I P Sbjct: 61 TVDADDVTLDGIVAAMQPDMLQLHGHESVGRVLEIKARYGLPVLKALSLRDRADLDQIGP 120 Query: 121 YLGIVDRFLLDAKPPAGSDLPGGNGISFDWRLLDALDGSVDYMLSGGLNAGNIADALALT 180 Y G+ DR LLDAKPPAGSDLPGGNG+SFDW+LL ALD S+DYMLSGGLNAGNIA+AL T Sbjct: 121 YSGVADRLLLDAKPPAGSDLPGGNGVSFDWKLLGALDASIDYMLSGGLNAGNIAEALRAT 180 Query: 181 GARAIDTSSGVESAPGIKDLTLMEAFFEA 209 AR ID SSGVESAPG+KD++L++ FF A Sbjct: 181 NARGIDISSGVESAPGLKDVSLIKEFFRA 209 Lambda K H 0.318 0.137 0.387 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: 187 Number of extensions: 4 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: 215 Length of database: 219 Length adjustment: 22 Effective length of query: 193 Effective length of database: 197 Effective search space: 38021 Effective search space used: 38021 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 (21.7 bits) S2: 45 (21.9 bits)
This GapMind analysis is from Jul 26 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