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_012402123.1 BPHY_RS14000 imidazole glycerol phosphate synthase cyclase subunit
Query= curated2:Q3Z6V7 (237 letters) >NCBI__GCF_000020045.1:WP_012402123.1 Length = 257 Score = 134 bits (337), Expect = 2e-36 Identities = 84/229 (36%), Positives = 127/229 (55%), Gaps = 20/229 (8%) Query: 3 IIPAIDILGGRCVRLLQGDYAQETVYSPDPVGTAMRWQSLGAPRLHVVDLDGAADGESVN 62 IIP +D+ GR V+ G E + DPV A R+ GA L +D+ +D + Sbjct: 7 IIPCLDVTAGRVVK---GVNFVELRDAGDPVEIARRYDEQGADELTFLDITATSDQRDLI 63 Query: 63 FELIREIANSALIPVEVGGGIRSMDTVKKLLTAGVDRVILGTVAVENPELVREICARY-A 121 +I +A+ IP+ VGGG+R+++ V++LL AG D+V + + AV NP+LVR+ +Y + Sbjct: 64 LPIIEAVASQVFIPLTVGGGVRAVEDVRRLLNAGADKVSMNSSAVANPQLVRDSTDKYGS 123 Query: 122 DSVAVSIDAR---------NGKVATRGWVNSTEVDALELARSMKKLGVKRFIYTDISRDG 172 + V+IDA+ +V T G +T +DA+E AR M +LG + T + RDG Sbjct: 124 QCIVVAIDAKRVSAEGETPRWEVFTHGGRKNTGLDAVEWARRMAELGAGEILLTSMDRDG 183 Query: 173 TLSEPNFAAIRDLISAINMPVIASGGVSSLSHLRLLKDIGAEGAIVGKA 221 T S + A R + A+++PVIASGGV SL HL A+G G+A Sbjct: 184 TKSGFDIALTRAVSDAVSIPVIASGGVGSLQHL-------ADGITQGRA 225 Score = 35.0 bits (79), Expect = 1e-06 Identities = 25/99 (25%), Positives = 43/99 (43%), Gaps = 2/99 (2%) Query: 31 DPVGTAMRWQSLGAPRLHVVDLDGAADGESVNFELIREIANSALIPVEVGGGIRSMDTVK 90 D V A R LGA + + +D + L R ++++ IPV GG+ S+ + Sbjct: 158 DAVEWARRMAELGAGEILLTSMDRDGTKSGFDIALTRAVSDAVSIPVIASGGVGSLQHLA 217 Query: 91 KLLTAG-VDRVILGTVAVENPELVREICARYADSVAVSI 128 +T G D V+ ++ V E C R+ +S+ Sbjct: 218 DGITQGRADAVLAASIFHYGEHTVGE-CKRFMADQGISV 255 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: 179 Number of extensions: 15 Number of successful extensions: 5 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: 237 Length of database: 257 Length adjustment: 24 Effective length of query: 213 Effective length of database: 233 Effective search space: 49629 Effective search space used: 49629 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