Align phosphoribosylanthranilate isomerase; EC 5.3.1.24 (characterized)
to candidate BPHYT_RS33880 BPHYT_RS33880 N-(5'-phosphoribosyl)anthranilate isomerase
Query= CharProtDB::CH_021917 (235 letters) >FitnessBrowser__BFirm:BPHYT_RS33880 Length = 244 Score = 312 bits (800), Expect = 3e-90 Identities = 163/230 (70%), Positives = 183/230 (79%) Query: 5 VSSRSLAESAESAVPPRTRIKLCGLSRPDDVLHAAALGADAIGLVFYAKSPRAVTIAQAA 64 +++ S + + A P RTRIKLCGLS+P DV A LGADAIGLVFY SPR+V++AQA Sbjct: 14 LANESHEGAQQQAAPHRTRIKLCGLSKPADVSRAIDLGADAIGLVFYPPSPRSVSVAQAV 73 Query: 65 ELARLAPPFVSVVGLFVNATAAEIEAVVRDVPLTLLQFHGDETPEQCDALGRAARLPWVR 124 EL PPFVSVVGLFVNATA I V +V LTLLQFHGDETPEQC++L A LPW+R Sbjct: 74 ELVHDVPPFVSVVGLFVNATADWIREVASNVGLTLLQFHGDETPEQCESLASVAGLPWLR 133 Query: 125 AVRVGPSTQSADLVESSLHYSKARGLLFDTLVPDYGGSGKVFDWSLIPAELARRAVLSGG 184 A+RV TQ ADLV+S+L YS A GLLFDT V YGG GKVFDWSLIPAELARRAVLSGG Sbjct: 134 ALRVAADTQPADLVKSALSYSSASGLLFDTHVEGYGGGGKVFDWSLIPAELARRAVLSGG 193 Query: 185 LNAQNVGDAIRQLRPFAVDVSSGIEVEGAKGVKDHARMAAFVRAVRDADA 234 LNAQNV +AI ++RP+AVDVSSGIE GAKGVKDHARMAAFVRAVR ADA Sbjct: 194 LNAQNVSEAIHRVRPYAVDVSSGIETPGAKGVKDHARMAAFVRAVRAADA 243 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: 209 Number of extensions: 5 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: 235 Length of database: 244 Length adjustment: 23 Effective length of query: 212 Effective length of database: 221 Effective search space: 46852 Effective search space used: 46852 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: 46 (22.3 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