Align N-(5'-phosphoribosyl)anthranilate isomerase 2; PRAI 2; EC 5.3.1.24 (uncharacterized)
to candidate 8500184 DvMF_0942 N-(5'phosphoribosyl)anthranilate isomerase (PRAI) (RefSeq)
Query= curated2:Q8PRX4 (226 letters) >FitnessBrowser__Miya:8500184 Length = 257 Score = 122 bits (307), Expect = 5e-33 Identities = 73/221 (33%), Positives = 118/221 (53%), Gaps = 7/221 (3%) Query: 3 IKVCGIKRVEDAVMAAYCGADAIGLVVGRKHNSDDFIDKHLAQKI--VRECP-PYISPVL 59 I+V G+ + +A+ + G A+GL + N++D + A+ + V P P + PV Sbjct: 22 IQVAGVHDMAEALALRHAGVHAMGLPLRLPVNAEDLTEADAARLVAEVERLPAPPLLPVG 81 Query: 60 VTELDDAEEISGLVHETGVTSVQLHSDCTVDSIISLRKTFPNIKIIKNFHVIGPG----V 115 +T + D E + G+ +QLH + LR+ P++ +IK+ V G + Sbjct: 82 ITYIADGAEAADFCRALGLRRLQLHGPVAATELARLRREIPDLFLIKSLVVRADGNLPEL 141 Query: 116 IHAMKPFESVVDAFILDTLDLANDKVGSTGLVHDWSISRKIVKEVSRPVILAGGLTPENV 175 + ++ + DAFI DT D A G+TGL HDW++S ++ + RPVILAGGL P+NV Sbjct: 142 LDTVRELAPLADAFITDTHDPATGADGATGLTHDWAVSAELARRSPRPVILAGGLNPDNV 201 Query: 176 GEAIRVVNPYGVDASSGLKDSNGFKDEMKVINFVHRAKNDF 216 AI V P GVDA +G++ +G K +++ FV A+ F Sbjct: 202 RAAILRVRPAGVDAHTGVEGPDGRKCPDRLLRFVAEAEQGF 242 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: 131 Number of extensions: 5 Number of successful extensions: 2 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: 257 Length adjustment: 23 Effective length of query: 203 Effective length of database: 234 Effective search space: 47502 Effective search space used: 47502 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