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 209220 DVU0286 imidazoleglycerol phosphate synthase, cyclase subunit
Query= curated2:B1YRW0 (251 letters) >MicrobesOnline__882:209220 Length = 259 Score = 91.7 bits (226), Expect = 1e-23 Identities = 62/209 (29%), Positives = 97/209 (46%), Gaps = 16/209 (7%) Query: 3 LIPAIDLKDGQCVRLKQGDMDQATIFSEDPAAMARKWVDLGARRLHLVDLNGAFAGKPKN 62 +IP +D++ G RL +G + + DP A AR++ + GA + D+ + + Sbjct: 6 IIPCLDVRAG---RLTKGVKFEGNVDIGDPVATARRYYEEGADEIVFYDITASHEDRGIF 62 Query: 63 LDAIEAILDEVGDEIPVQLGGGIRSLETVEKYLDAGLSYVIIGTAAVKDPGFLRDACTAF 122 LD +E + E+ IP +GGGI +++ + L AG V + + AVK P + AF Sbjct: 63 LDVVERVASEIF--IPFSVGGGINTVDDMRAVLMAGAEKVSVNSGAVKTPDIISQGAAAF 120 Query: 123 AGN-IIVGLDAKDGK----------VATDGWSKLTGHEVIDLALKFEDYGVESIVYTDIG 171 I+VG+D K + + G K G + I+ A E G + I Sbjct: 121 GSQAIVVGMDVKQVEKSATIPSGYEIVIHGGRKYMGMDAIEWAKTCESLGAGELCVNSID 180 Query: 172 RDGMLQGINIEATVKLAQAVGIPVIASGG 200 DG G + T ++ AV IPVIASGG Sbjct: 181 ADGTKDGYELTLTRMISDAVTIPVIASGG 209 Score = 30.8 bits (68), Expect = 3e-05 Identities = 23/86 (26%), Positives = 44/86 (51%), Gaps = 6/86 (6%) Query: 126 IIVGLDAKDGKVATDGWSKLTGH----EVIDLALKFEDYGVESIVYTDIGRDGMLQGINI 181 II LD + G++ T G K G+ + + A ++ + G + IV+ DI +GI + Sbjct: 6 IIPCLDVRAGRL-TKG-VKFEGNVDIGDPVATARRYYEEGADEIVFYDITASHEDRGIFL 63 Query: 182 EATVKLAQAVGIPVIASGGLSNLADI 207 + ++A + IP GG++ + D+ Sbjct: 64 DVVERVASEIFIPFSVGGGINTVDDM 89 Lambda K H 0.318 0.139 0.402 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: 182 Number of extensions: 13 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 251 Length of database: 259 Length adjustment: 24 Effective length of query: 227 Effective length of database: 235 Effective search space: 53345 Effective search space used: 53345 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: 41 (21.7 bits) S2: 47 (22.7 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