Align N-(5'-phosphoribosyl)anthranilate isomerase 2; PRAI 2; EC 5.3.1.24 (uncharacterized)
to candidate 207989 N-(5-phosphoribosyl)anthranilate isomerase
Query= curated2:Q8PRX4 (226 letters) >MicrobesOnline__882:207989 Length = 308 Score = 143 bits (360), Expect = 4e-39 Identities = 87/221 (39%), Positives = 124/221 (56%), Gaps = 8/221 (3%) Query: 3 IKVCGIKRVEDAVMAAYCGADAIGLVVGRKHNSDDFIDKHLAQKIVRECPPYISPVLVTE 62 I++ G+ ++A + A CG A+GL + N++D ID+ A ++V PP I+PV +T Sbjct: 83 IQIAGVHDADEACLLARCGVHAVGLPLRLPVNAED-IDEAAAARLVAGLPPVITPVAITY 141 Query: 63 LDDAEEISGLVHETGVTSVQLHSDCTVDSIISLRKTFPNIKIIKNFHVI-------GPGV 115 +DDA+E GV +QLH VD + LR+ P++ IIK+ V G + Sbjct: 142 MDDADEADAFCTMLGVGHLQLHGAIRVDEMARLRRLRPDLFIIKSLVVREHGGMDNGETL 201 Query: 116 IHAMKPFESVVDAFILDTLDLANDKVGSTGLVHDWSISRKIVKEVSRPVILAGGLTPENV 175 + ++ F VDAFI DT G+TG HDW++S +V+ RPVILAGGL P NV Sbjct: 202 MGDVQAFAPHVDAFITDTFAPETGASGATGKTHDWAVSAALVRLSPRPVILAGGLHPGNV 261 Query: 176 GEAIRVVNPYGVDASSGLKDSNGFKDEMKVINFVHRAKNDF 216 EA+R V P GVDA +G++ +G KDE V FV A F Sbjct: 262 REAVRRVCPAGVDAHTGVEGPDGRKDEGLVRRFVAEALAGF 302 Lambda K H 0.320 0.138 0.402 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: 194 Number of extensions: 11 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: 226 Length of database: 308 Length adjustment: 25 Effective length of query: 201 Effective length of database: 283 Effective search space: 56883 Effective search space used: 56883 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: 47 (22.7 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