Align N-(5'-phosphoribosyl)anthranilate isomerase; Short=PRAI; EC 5.3.1.24 (characterized, see rationale)
to candidate WP_012568239.1 RC1_RS14790 phosphoribosylanthranilate isomerase
Query= uniprot:A0A0H3CC53_CAUVN (219 letters) >NCBI__GCF_000016185.1:WP_012568239.1 Length = 214 Score = 202 bits (515), Expect = 3e-57 Identities = 100/204 (49%), Positives = 145/204 (71%), Gaps = 2/204 (0%) Query: 9 KICGLSTPETVKAAFDGAAAFLGFVFFDKSPRNVAPEVAARLVEPVRGRGVQTVAVTVDP 68 KICG++ P+ + AA G A ++G VF+++SPR+VAPE+AA L V GV+ V + VDP Sbjct: 6 KICGINRPDALAAAVAGGARYVGLVFYERSPRHVAPELAAELARQVP-TGVRVVGLFVDP 64 Query: 69 DDALIDRLMATMRPDLIQVHGKETPSRVREIAARAGVGVIKAFSVSSSADVDQAAAFDGV 128 D +++R++ ++ DLIQ+HG+ETP RV + A G+ V+KA V+ +AD+D+AAA++G Sbjct: 65 DALMLERVLGSVPLDLIQLHGEETPERVAAVRAAHGIEVMKAVKVAGAADLDRAAAYEGA 124 Query: 129 AQHLMFDARPVEG-SVLPGGTGARFDWGLLAGRRFSRPHFLAGGLDPWNVGEAIKTSGTP 187 L+FDA+ +G + LPGG G FDW LLAGR ++RP L+GGL+ N+ EA++ +G Sbjct: 125 CDRLLFDAKAPKGVAALPGGNGLSFDWTLLAGRTWARPWMLSGGLNAGNLAEAVRATGAT 184 Query: 188 LVDVSSGVERGPGLKDPALISAFL 211 VDVSSGVE PG KDPAL++ FL Sbjct: 185 AVDVSSGVEDRPGHKDPALVAGFL 208 Lambda K H 0.320 0.136 0.401 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: 170 Number of extensions: 10 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: 219 Length of database: 214 Length adjustment: 22 Effective length of query: 197 Effective length of database: 192 Effective search space: 37824 Effective search space used: 37824 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: 45 (21.9 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