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_012568439.1 RC1_RS15790 imidazole glycerol phosphate synthase subunit HisF
Query= curated2:Q0W0J3 (240 letters) >NCBI__GCF_000016185.1:WP_012568439.1 Length = 258 Score = 124 bits (311), Expect = 2e-33 Identities = 81/243 (33%), Positives = 135/243 (55%), Gaps = 16/243 (6%) Query: 5 VIPAIDLKGGKCVQLVQGVPGTEMVSIDDAVEVAAGWVGQGAKTLHIIDLDGAFSGSRKN 64 VIP +D+K G+ +V+GV ++V D VE A + GA L +D+ A S +R+ Sbjct: 6 VIPCLDVKDGR---VVKGVNFVDLVDAGDPVEQARLYDAAGADELTFLDIT-ASSDNRET 61 Query: 65 AY-IMEDIVSKFDVDVQVGGGIRDYETAKYLLSLGIDRVILGTAAIKNPDLVRQLADEFG 123 Y ++ + + + VGGG+R E + LL G D+V + TAA+ PD VR+ A++FG Sbjct: 62 IYDVVRRTAEQVFMPLTVGGGVRTVEDIRRLLLAGADKVSINTAAVHRPDFVREGAEKFG 121 Query: 124 SETVMVSLDSK----------QGEVVIEGWTESSGKTTNEMGKFFSEIGAGSILYTNVDV 173 S+ ++V++D+K + EV G +G + + +E+GAG IL T++D Sbjct: 122 SQCIVVAIDAKAVAPGPDGAPRWEVFTHGGRTPTGLDAVDWARRMAELGAGEILLTSMDR 181 Query: 174 EGLLKGVNEDPVRSLVNSVTIPVIASGGVAKIDDLVK-IKNTGAAGVVVGSALYKGLFTL 232 +G G + R++ ++V +PVIASGGV +D LV I++ A V+ S + G F++ Sbjct: 182 DGTKAGFDIGLTRAVADAVPVPVIASGGVGTLDHLVAGIRDGHATAVLAASIFHFGTFSV 241 Query: 233 REA 235 +A Sbjct: 242 GQA 244 Score = 33.5 bits (75), Expect = 4e-06 Identities = 19/86 (22%), Positives = 37/86 (43%) Query: 153 EMGKFFSEIGAGSILYTNVDVEGLLKGVNEDPVRSLVNSVTIPVIASGGVAKIDDLVKIK 212 E + + GA + + ++ + D VR V +P+ GGV ++D+ ++ Sbjct: 34 EQARLYDAAGADELTFLDITASSDNRETIYDVVRRTAEQVFMPLTVGGGVRTVEDIRRLL 93 Query: 213 NTGAAGVVVGSALYKGLFTLREAIDK 238 GA V + +A +RE +K Sbjct: 94 LAGADKVSINTAAVHRPDFVREGAEK 119 Lambda K H 0.315 0.136 0.378 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: 167 Number of extensions: 11 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 240 Length of database: 258 Length adjustment: 24 Effective length of query: 216 Effective length of database: 234 Effective search space: 50544 Effective search space used: 50544 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 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