Align N-(5'-phosphoribosyl)anthranilate isomerase 2; PRAI 2; EC 5.3.1.24 (uncharacterized)
to candidate WP_090218246.1 CV091_RS10410 phosphoribosylanthranilate isomerase
Query= curated2:Q8PRX4 (226 letters) >NCBI__GCF_002796795.1:WP_090218246.1 Length = 229 Score = 111 bits (278), Expect = 1e-29 Identities = 69/226 (30%), Positives = 121/226 (53%), Gaps = 4/226 (1%) Query: 3 IKVCGIKRVEDAVMAAYCGADAIGLVVGRKHNSDDFIDKHLAQKIVRECPPYISPVLVTE 62 ++V GI ++A + GAD IG + DD I + A+ I++ VL++ Sbjct: 5 VQVAGIIDSKEAELCFANGADWIGFPLRLPSGKDD-ISEADAKAIIKTLKAPQRAVLISY 63 Query: 63 LDDAEEISGLVHETGVTSVQLHSDCTVDSIISLRKTFPNIKIIKNFHVIG---PGVIHAM 119 + A E+S E G+ +VQLH D +++ + LR+ P++ ++K+ V P + + Sbjct: 64 MTTAAEVSQFCDELGLDAVQLHGDISMEELAKLRQMRPDLYLLKSLVVSADNLPALRQLI 123 Query: 120 KPFESVVDAFILDTLDLANDKVGSTGLVHDWSISRKIVKEVSRPVILAGGLTPENVGEAI 179 +D +I DT D G+TG+ HDW++S ++V+ +P+++AGGL+P+NV +AI Sbjct: 124 DDSAEYIDMYITDTFDPKTGAKGATGMTHDWNVSAELVRHSPKPLMMAGGLSPDNVYDAI 183 Query: 180 RVVNPYGVDASSGLKDSNGFKDEMKVINFVHRAKNDFFKVRNLSLE 225 V P VDA S L+ ++ K K+ F AK F ++ L+ + Sbjct: 184 MQVRPAAVDAHSLLEGTDKRKSAEKMRVFSAEAKRAFSEMSVLAAQ 229 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: 121 Number of extensions: 7 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: 229 Length adjustment: 22 Effective length of query: 204 Effective length of database: 207 Effective search space: 42228 Effective search space used: 42228 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 Jul 26 2024. The underlying query database was built on Jul 25 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