Align Phosphoribosyl isomerase A; 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; EC 5.3.1.16; N-(5'-phosphoribosyl)anthranilate isomerase; PRAI; EC 5.3.1.24; Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (uncharacterized)
to candidate 3609190 Dshi_2576 imidazoleglycerol phosphate synthase, cyclase subunit (RefSeq)
Query= curated2:P60583 (243 letters) >FitnessBrowser__Dino:3609190 Length = 253 Score = 93.6 bits (231), Expect = 3e-24 Identities = 76/253 (30%), Positives = 119/253 (47%), Gaps = 26/253 (10%) Query: 4 LLPAVDVVDGRAVRLVQG----KAGSETEYGSALDAALGWQRDGAEWIHLVDLDAAF-GR 58 ++P +DV DGR V+ V AG E A DAA GA+ + +D+ A R Sbjct: 6 VIPCLDVADGRVVKGVNFVDLVDAGDPVESAKAYDAA------GADELCFLDIHATNENR 59 Query: 59 GSNRELLAEVVGKLDVRVELSGGIRDDDSLAAALATGCARVNLGTAALENPQWCARAIGE 118 G+ +L + + + + GG+R + + L G +V+ +AA+ +P ARA + Sbjct: 60 GTMYDLATRTAEQCFMPLTIGGGVRTTEDVRNLLLAGADKVSFNSAAVADPDVIARAADK 119 Query: 119 HGDKVAVGLDVQIIDGQHRLRGRGWE--TDGG------DLWEVLERLERQGCSRYVVTDV 170 G + V ID + GR WE T GG D E + + +G ++T + Sbjct: 120 FGSQCIVCA----IDAKTVAPGR-WEIFTHGGRKPTGIDAVEFAKTVVEKGAGEILLTSM 174 Query: 171 TKDGTLGGPNLDLLGAVADRTDAPVIASGGVSSLDDLRAIATLTGRGVEGAIVGKALYAG 230 +DGT G N+ L A++D PVIASGGV +LD L + +T G + + G Sbjct: 175 DRDGTKQGFNIALTRAISDAVSVPVIASGGVGTLDHL--VEGVTEGGASAVLAASIFHFG 232 Query: 231 RFTLPQALAAVAE 243 FT+ +A +AE Sbjct: 233 EFTIREAKEHMAE 245 Lambda K H 0.318 0.138 0.407 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: 179 Number of extensions: 10 Number of successful extensions: 5 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: 243 Length of database: 253 Length adjustment: 24 Effective length of query: 219 Effective length of database: 229 Effective search space: 50151 Effective search space used: 50151 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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