Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_009566362.1 RSPH17029_RS04675 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase
Query= BRENDA::P16250 (240 letters) >NCBI__GCF_000015985.1:WP_009566362.1 Length = 239 Score = 158 bits (399), Expect = 1e-43 Identities = 95/236 (40%), Positives = 131/236 (55%), Gaps = 5/236 (2%) Query: 6 LLPAVDVRDGQAVRLVHGESGTETSYGS-PLEAALAWQRSGAEWLHLVDLDAAF-GTGDN 63 L PA+D++DGQ VRL+ GE T +G P A A++ +G EW+HLVDL+ AF G N Sbjct: 3 LYPAIDLKDGQCVRLLRGEMEAATVFGDDPAAQAAAFEAAGCEWVHLVDLNGAFAGRPVN 62 Query: 64 RALIAEVAQAMDIKVELSGGIRDDDTLAAALATGCTRVNLGTAALETPEWVAKVIAEHGD 123 A + + + + +L GGIRD T+A L G RV LGT A+E P V + Sbjct: 63 AAAVEAILARIAVPAQLGGGIRDMATIALWLEKGLARVILGTVAVENPGLVREAARAFPG 122 Query: 124 KIAVGLDVRGTTLRGRGWTRDGGDLYETLDR-LNKEGCARYVVTDIAKDGTLQGPNLELL 182 ++AVG+D R + +GW + + L R G A + TDI +DG + GPN+E Sbjct: 123 RVAVGIDARKGRVATKGWATETDVMATDLARSFEDAGVAAIIYTDIDRDGAMAGPNIEAT 182 Query: 183 KNVCAATDRPVVASGGVSSLDDLRAIAGLVPAGVEGAIVGKALYAKAFTLEEALEA 238 + A PV+ASGGVSSL DL A+ + GAI G+ALY A L +AL+A Sbjct: 183 DALARAVSIPVIASGGVSSLADLLALRD--TGSIAGAISGRALYDGALDLTQALQA 236 Lambda K H 0.315 0.133 0.385 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: 162 Number of extensions: 13 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: 240 Length of database: 239 Length adjustment: 23 Effective length of query: 217 Effective length of database: 216 Effective search space: 46872 Effective search space used: 46872 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: 42 (22.0 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Apr 10 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