Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_011940835.1 GURA_RS20620 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= BRENDA::P16250 (240 letters) >NCBI__GCF_000016745.1:WP_011940835.1 Length = 245 Score = 161 bits (407), Expect = 1e-44 Identities = 95/238 (39%), Positives = 140/238 (58%), Gaps = 5/238 (2%) Query: 6 LLPAVDVRDGQAVRLVHGESGTETSY-GSPLEAALAWQRSGAEWLHLVDLDAAF-GTGDN 63 ++PA+D+++G+ VRL G +T + +P E A W+R G E LH+VDLD AF G N Sbjct: 3 VIPAIDLKEGKCVRLEQGLMDKDTVFCDNPAEQAREWERQGGELLHIVDLDGAFAGKPAN 62 Query: 64 RALIAEVAQAMDIKVELSGGIRDDDTLAAALATGCTRVNLGTAALETPEWVAKVIAEHGD 123 ++ I + +A+ I +L GGIRD +T+ A L G +RV LGTAA P+ V + Sbjct: 63 KSAIEAIVKAVRIPTQLGGGIRDIETIKAYLDLGLSRVILGTAAQRNPKLVEEACKLFPG 122 Query: 124 KIAVGLDVRGTTLRGRGWTRDGGDLYET-LDRLNKE-GCARYVVTDIAKDGTLQGPNLEL 181 +I VG+D + + +GW + D+Y L RL + G + TDI++DG +QGPN++ Sbjct: 123 RIVVGIDAKNGLVAVQGWA-EVTDVYAVDLARLFEGYGVTAVIYTDISRDGMMQGPNIDA 181 Query: 182 LKNVCAATDRPVVASGGVSSLDDLRAIAGLVPAGVEGAIVGKALYAKAFTLEEALEAT 239 + + A PV+ASGGVSSL D+ + + AGV G I GKA+Y A L EA+ T Sbjct: 182 TRALAEAISIPVIASGGVSSLKDIENLMAVESAGVTGVITGKAIYTGAIKLAEAVALT 239 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: 164 Number of extensions: 13 Number of successful extensions: 4 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: 245 Length adjustment: 23 Effective length of query: 217 Effective length of database: 222 Effective search space: 48174 Effective search space used: 48174 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 12 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