Align 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; EC 5.3.1.16; Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (uncharacterized)
to candidate WP_011802492.1 PNAP_RS15615 imidazole glycerol phosphate synthase cyclase subunit
Query= curated2:A5V9V9 (243 letters) >NCBI__GCF_000015505.1:WP_011802492.1 Length = 253 Score = 85.9 bits (211), Expect = 7e-22 Identities = 68/220 (30%), Positives = 104/220 (47%), Gaps = 9/220 (4%) Query: 5 VFPAIDLKGGQVVRLAEGDMDRATVYGDDPADQARRFAEAGAEWLHVVDLDGAFAGRAVN 64 V P + LK G +V+ + + Y DP + R F + + L V+D++ + A R N Sbjct: 6 VIPCLLLKNGGLVKTKKFQDPK---YVGDPINVIRIFNDKEVDELIVLDIEASKAQREPN 62 Query: 65 AEAVEAIIKAFPGKVELGGGIRDRAGIDRWLALGVERVIIGTAALQNPDLVREAAKELPG 124 E +E + GGGI R LGVE+V I T AL + LVR+ A Sbjct: 63 YELIEQFAGECFMPLCYGGGISTVEQAKRLFTLGVEKVCIQTWALADLQLVRDIADRYGS 122 Query: 125 R-IVVGVDARDGFVATHGWAEVSTVGITDLA-----DRFADAGVASLLFTDVGRDGLLKG 178 + +VV VD + A+H ST + DL ++ AG ++ T V RDG L G Sbjct: 123 QSVVVSVDIKKNLFASHRLYASSTGKMLDLPWQDFLNKAVAAGAGEIMLTAVDRDGTLAG 182 Query: 179 CNVEATVALARHASIPVIASGGVASIADIAALVPHAGDGI 218 ++ A ++ IP+IA+GG A+++D+ A V I Sbjct: 183 MDLALIHAASQSCPIPLIAAGGAATLSDLRAAVDAGASAI 222 Lambda K H 0.321 0.140 0.406 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: 146 Number of extensions: 10 Number of successful extensions: 3 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 ( 7.4 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 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