Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_013536927.1 THEAM_RS00875 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= BRENDA::P16250 (240 letters) >NCBI__GCF_000185805.1:WP_013536927.1 Length = 244 Score = 165 bits (418), Expect = 7e-46 Identities = 96/238 (40%), Positives = 137/238 (57%), Gaps = 11/238 (4%) Query: 6 LLPAVDVRDGQAVRLVHGESGTETSY-GSPLEAALAWQRSGAEWLHLVDLDAAF-GTGDN 63 ++PAVD++ G+ VRL G++ E Y +P+E A W+ GA +H+VDLD AF G N Sbjct: 4 VIPAVDIKGGKCVRLYQGKADAEKVYFENPVEVAKRWEEEGASIIHVVDLDGAFEGVPKN 63 Query: 64 RALIAEVAQAMDIKVELSGGIRDDDTLAAALATGCTRVNLGTAALETPEWVAKVIAEHGD 123 ++ E+ Q + I V+ GG+R L G +RV +GT A+E PE K E D Sbjct: 64 LPIVKEIVQELSIPVQFGGGVRTRKALEELFKAGVSRVVVGTVAVEEPELFKKWTEEFPD 123 Query: 124 KIAVGLDVRGTTLRGRGWTRDGG----DLYETLDRLNKEGCARYVVTDIAKDGTLQGPNL 179 K+ VG+D + RGW G +L LD+L G +V TDI++DGTL PN Sbjct: 124 KLVVGIDAKNGIATTRGWVELSGIPATELARNLDQLPIWG---FVYTDISRDGTLTSPNF 180 Query: 180 ELLKNVCAATDRPVVASGGVSSLDDLRAIAGLVPAGVEGAIVGKALYAKAFTLEEALE 237 E ++ +A + PV+ASGGVSS +DL+ ++ + V GAIVGKALY L+EA+E Sbjct: 181 EEVEKFASAVEHPVIASGGVSSPEDLKRLSKI--KNVAGAIVGKALYEGKVNLKEAIE 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: 154 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: 240 Length of database: 244 Length adjustment: 23 Effective length of query: 217 Effective length of database: 221 Effective search space: 47957 Effective search space used: 47957 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