Align N-(5'-phosphoribosyl)anthranilate isomerase; Short=PRAI; EC 5.3.1.24 (characterized, see rationale)
to candidate WP_015928871.1 MNOD_RS10630 phosphoribosylanthranilate isomerase
Query= uniprot:TRPF_RHIME (215 letters) >NCBI__GCF_000022085.1:WP_015928871.1 Length = 222 Score = 196 bits (499), Expect = 2e-55 Identities = 102/208 (49%), Positives = 139/208 (66%), Gaps = 1/208 (0%) Query: 5 VKICGLKTAEAVERAVALGASHVGFIFFPKSPRNIEPDDAGRLAARARGRAKIVAVTVDA 64 VKICGL T E ++ A+A GA +G + F +SPR+++ L+ RA+GRA+ V + VD Sbjct: 8 VKICGLSTPETLDAALAAGADLIGLVHFARSPRHVDLATGAALSRRAQGRAERVVLLVDP 67 Query: 65 DNDGLDEIVSALDPDVLQLHGSETPERVLSIKALYGLPVMKALAVREASDLERIDPYLGI 124 D+ LD +++ LDPD +QLHG E+PER +++A G V+KAL V +DL R+ Y G Sbjct: 68 DDALLDAVMAGLDPDWIQLHGGESPERAAAVRARTGRRVLKALGVATLADLARVADYAGA 127 Query: 125 VDRFLLDAKPPAGSDLPGGNGISFDWRLLDALDGSVDYMLSGGLNAGNIADALALTGARA 184 DR LLDAKP G+ LPGGNG +FDWRL+ + +MLSGGL +A+A+ALTGA A Sbjct: 128 ADRILLDAKPAPGA-LPGGNGQAFDWRLIREARLAPTFMLSGGLTPATVAEAVALTGAAA 186 Query: 185 IDTSSGVESAPGIKDLTLMEAFFEAVRR 212 +D SSGVE +PG KD L+ AF A R+ Sbjct: 187 VDVSSGVERSPGRKDPDLIRAFVAAARQ 214 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: 182 Number of extensions: 12 Number of successful extensions: 2 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: 222 Length adjustment: 22 Effective length of query: 193 Effective length of database: 200 Effective search space: 38600 Effective search space used: 38600 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 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