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_011940834.1 GURA_RS20615 imidazole glycerol phosphate synthase cyclase subunit
Query= curated2:Q3Z6V7 (237 letters) >NCBI__GCF_000016745.1:WP_011940834.1 Length = 253 Score = 129 bits (325), Expect = 4e-35 Identities = 75/210 (35%), Positives = 118/210 (56%), Gaps = 10/210 (4%) Query: 3 IIPAIDILGGRCVRLLQGDYAQETVYSPDPVGTAMRWQSLGAPRLHVVDLDGAADGESVN 62 IIP +D+ GGR V+ +Q E + DPV A + GA L +D+ ++D + Sbjct: 6 IIPCLDVKGGRVVKGVQ---FLELRDAGDPVEIAEIYDRQGADELTFLDITASSDARDII 62 Query: 63 FELIREIANSALIPVEVGGGIRSMDTVKKLLTAGVDRVILGTVAVENPELVREICARY-A 121 +++R A +P+ VGGG+R+++ +++LL AG D+V + T AV PE V+E R+ + Sbjct: 63 IDVVRRTAERVFMPLTVGGGVRTVEDIRRLLNAGADKVSINTAAVHRPEFVKEAAERFGS 122 Query: 122 DSVAVSIDAR------NGKVATRGWVNSTEVDALELARSMKKLGVKRFIYTDISRDGTLS 175 V+IDAR +V T G N+T +DA+E A+ M+ G + T + RDGT Sbjct: 123 QCTVVAIDARRVPGEDRWEVYTHGGRNATGIDAVEWAQRMEAYGSGEILLTSMDRDGTKD 182 Query: 176 EPNFAAIRDLISAINMPVIASGGVSSLSHL 205 + R + A+++PVIASGGV +L HL Sbjct: 183 GYDLPLTRAVADAVSIPVIASGGVGNLEHL 212 Score = 32.3 bits (72), Expect = 9e-06 Identities = 17/75 (22%), Positives = 32/75 (42%) Query: 147 DALELARSMKKLGVKRFIYTDISRDGTLSEPNFAAIRDLISAINMPVIASGGVSSLSHLR 206 D +E+A + G + DI+ + +R + MP+ GGV ++ +R Sbjct: 31 DPVEIAEIYDRQGADELTFLDITASSDARDIIIDVVRRTAERVFMPLTVGGGVRTVEDIR 90 Query: 207 LLKDIGAEGAIVGKA 221 L + GA+ + A Sbjct: 91 RLLNAGADKVSINTA 105 Score = 30.8 bits (68), Expect = 3e-05 Identities = 16/66 (24%), Positives = 32/66 (48%) Query: 31 DPVGTAMRWQSLGAPRLHVVDLDGAADGESVNFELIREIANSALIPVEVGGGIRSMDTVK 90 D V A R ++ G+ + + +D + + L R +A++ IPV GG+ +++ + Sbjct: 154 DAVEWAQRMEAYGSGEILLTSMDRDGTKDGYDLPLTRAVADAVSIPVIASGGVGNLEHLY 213 Query: 91 KLLTAG 96 T G Sbjct: 214 DGFTKG 219 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: 164 Number of extensions: 9 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 237 Length of database: 253 Length adjustment: 24 Effective length of query: 213 Effective length of database: 229 Effective search space: 48777 Effective search space used: 48777 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 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