Align phosphoribosylanthranilate isomerase; EC 5.3.1.24 (characterized)
to candidate WP_027456317.1 K420_RS0100480 phosphoribosylanthranilate isomerase
Query= CharProtDB::CH_021917 (235 letters) >NCBI__GCF_000519045.1:WP_027456317.1 Length = 211 Score = 221 bits (562), Expect = 1e-62 Identities = 121/214 (56%), Positives = 143/214 (66%), Gaps = 9/214 (4%) Query: 21 RTRIKLCGLSRPDDVLHAAALGADAIGLVFYAKSPRAVTIAQAAELARLAPPFVSVVGLF 80 +TRIK+CGL+R DV A GADAIG V Y SPR VT +AAELA+ PPFV +VGLF Sbjct: 2 KTRIKICGLTREADVEAAVEAGADAIGFVLYPASPRYVTPRRAAELAKRIPPFVDIVGLF 61 Query: 81 VNATAAEIEAVVRDVPLTLLQFHGDETPEQCDALGRAARLPWVRAVRVGPSTQSADLVES 140 VN + + A ++P+ LLQFHGDE C R PW+RA RV P DLVE Sbjct: 62 VNEASEVVRAACSELPINLLQFHGDEDAAYCRQFAR----PWLRAARVRP---GLDLVEF 114 Query: 141 SLHYSKARGLLFDTLVPDYGGSGKVFDWSLIPAELARRAVLSGGLNAQNVGDAIRQLRPF 200 + Y ARGLL D V YGG G VFDW+LIP +L VLSGGL+ NVGDAIR++RP Sbjct: 115 ARSYHDARGLLLDAFVEGYGGGGHVFDWTLIPPDLPGYLVLSGGLHDANVGDAIRRVRPA 174 Query: 201 AVDVSSGIEVEGAKGVKDHARMAAFVRAVRDADA 234 AVDVSSG+EV +KG+KDH +M AFV AVR ADA Sbjct: 175 AVDVSSGVEV--SKGIKDHDKMRAFVAAVRAADA 206 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: 163 Number of extensions: 13 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: 211 Length adjustment: 22 Effective length of query: 213 Effective length of database: 189 Effective search space: 40257 Effective search space used: 40257 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 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