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 Ga0059261_1048 Ga0059261_1048 imidazoleglycerol phosphate synthase, cyclase subunit
Query= curated2:Q3Z6V7 (237 letters) >FitnessBrowser__Korea:Ga0059261_1048 Length = 255 Score = 120 bits (302), Expect = 2e-32 Identities = 74/242 (30%), Positives = 124/242 (51%), Gaps = 10/242 (4%) Query: 3 IIPAIDILGGRCVRLLQGDYAQETVYSPDPVGTAMRWQSLGAPRLHVVDLDGAADGESVN 62 +IP +D+ GR V+ + ++ + DPV A + + GA L +D+ + + Sbjct: 7 VIPCLDVANGRVVKGVNFVNLRD---AGDPVEQARAYDAAGADELCFLDITASHEARGTI 63 Query: 63 FELIREIANSALIPVEVGGGIRSMDTVKKLLTAGVDRVILGTVAVENPELVREICARY-A 121 +++R A +P+ VGGG+RS + + LL AG D+V + + AV PE+V EI R+ + Sbjct: 64 IDVVRRTAEVCFMPLTVGGGVRSAEDARALLLAGADKVAVNSAAVTRPEVVSEIAERFGS 123 Query: 122 DSVAVSIDAR-----NGKVATRGWVNSTEVDALELARSMKKLGVKRFIYTDISRDGTLSE 176 + S+DAR +V T G T +DA+E A + KLG + T + RDGT Sbjct: 124 QCIVASVDARRVADGRWEVFTHGGRKPTGIDAVEHALHLAKLGAGELLLTSMDRDGTRDG 183 Query: 177 PNFAAIRDLISAINMPVIASGGVSSLSHLRL-LKDIGAEGAIVGKAIYTGDLNLKRAFEE 235 + IR + + +PV+ASGGV +L HL ++D A + + G+ ++ A Sbjct: 184 YDLDLIRTIADRVRVPVVASGGVGNLDHLVAGIRDGHASAVLAASIFHFGEASIVGAHAA 243 Query: 236 LS 237 L+ Sbjct: 244 LA 245 Lambda K H 0.318 0.136 0.384 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: 185 Number of extensions: 12 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: 237 Length of database: 255 Length adjustment: 24 Effective length of query: 213 Effective length of database: 231 Effective search space: 49203 Effective search space used: 49203 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: 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