Align N-(5'-phosphoribosyl)anthranilate isomerase; Short=PRAI; EC 5.3.1.24 (characterized, see rationale)
to candidate GFF475 PGA1_c04860 N-(5'-phosphoribosyl)anthranilate isomerase TrpF
Query= uniprot:TRPF_RHIME (215 letters) >FitnessBrowser__Phaeo:GFF475 Length = 217 Score = 201 bits (512), Expect = 7e-57 Identities = 105/210 (50%), Positives = 140/210 (66%), Gaps = 1/210 (0%) Query: 1 MKTEVKICGLKTAEAVERAVALGASHVGFIFFPKSPRNIEPDDAGRLAARARGRAKIVAV 60 M VKICGLKT + + A GA+++GF FF KSPR++ ++A LA A VA+ Sbjct: 2 MDIRVKICGLKTPQDIVAAADAGAAYIGFNFFAKSPRSVTVEEATALAVEAPVGLCKVAL 61 Query: 61 TVDADNDGLDEIVSALDPDVLQLHGSETPERVLSIKALYGLPVMKALAVREASDLERIDP 120 V+ D+ LDEI SA+ D++QLHG ETPERV +KA YGLPVMK L V A D++RI+ Sbjct: 62 VVNPDDAMLDEITSAVPLDMIQLHGQETPERVAEVKARYGLPVMKVLGVSTAEDIQRIEA 121 Query: 121 YLGIVDRFLLDAKPPAGSDLPGGNGISFDWRLLDALD-GSVDYMLSGGLNAGNIADALAL 179 Y + D+ L+DAK P G+ LPGGNG++FDW LL +ML+GGL N+A+A+ + Sbjct: 122 YEAVADQILVDAKAPKGAVLPGGNGVTFDWGLLARKKYWRTPWMLAGGLTPENVAEAIRV 181 Query: 180 TGARAIDTSSGVESAPGIKDLTLMEAFFEA 209 TGAR +D +SG ESAPG+KD + AF EA Sbjct: 182 TGARQVDVASGAESAPGVKDPARIRAFCEA 211 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: 151 Number of extensions: 5 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: 215 Length of database: 217 Length adjustment: 22 Effective length of query: 193 Effective length of database: 195 Effective search space: 37635 Effective search space used: 37635 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 Apr 09 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