Align phosphoribosylanthranilate isomerase; EC 5.3.1.24 (characterized)
to candidate PfGW456L13_3940 Phosphoribosylanthranilate isomerase (EC 5.3.1.24)
Query= CharProtDB::CH_021917 (235 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3940 Length = 208 Score = 200 bits (509), Expect = 2e-56 Identities = 105/209 (50%), Positives = 143/209 (68%), Gaps = 10/209 (4%) Query: 23 RIKLCGLSRPDDVLHAAALGADAIGLVFYAKSPRAVTIAQAAELARLAPPFVSVVGLFVN 82 R K+CG++R +D L A GADAIG VFYAKSPRAVT+ QA + + PPFV+ VGLFVN Sbjct: 5 RSKICGITRIEDALAAVEAGADAIGFVFYAKSPRAVTVQQARSIIKALPPFVTTVGLFVN 64 Query: 83 ATAAEIEAVVRDVPLTLLQFHGDETPEQCDALGRAARLPWVRAVRVGPSTQSADLVESSL 142 A+ E+ ++ VPL LLQFHGDET +C+ R P+++A+RV D+ + Sbjct: 65 ASRCELGEILDAVPLDLLQFHGDETAAECEGWHR----PYIKALRV---KAGDDIAAACD 117 Query: 143 HYSKARGLLFDTLVPDY-GGSGKVFDWSLIPAELARRAVLSGGLNAQNVGDAIRQLRPFA 201 Y+ A G+L DT V GG+G+ FDWSLIP L++ +L+GGL NV +AI ++RP+A Sbjct: 118 AYASASGILLDTYVEGVPGGTGEAFDWSLIPQGLSKPVILAGGLTPDNVAEAIARVRPYA 177 Query: 202 VDVSSGIEVEGAKGVKDHARMAAFVRAVR 230 VDVS G VE +KG+KDHA++ AF++AVR Sbjct: 178 VDVSGG--VEASKGIKDHAKIQAFIKAVR 204 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: 151 Number of extensions: 9 Number of successful extensions: 4 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: 208 Length adjustment: 22 Effective length of query: 213 Effective length of database: 186 Effective search space: 39618 Effective search space used: 39618 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 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