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 16133 b2025 imidazole glycerol phosphate synthase subunit HisF (NCBI)
Query= curated2:A0LCF2 (249 letters) >FitnessBrowser__Keio:16133 Length = 258 Score = 94.4 bits (233), Expect = 2e-24 Identities = 64/212 (30%), Positives = 105/212 (49%), Gaps = 14/212 (6%) Query: 2 RIIPAIDLKDGQCVRLFKGDMDQNTVYSDNPGETAKQWAEQGAERMHVVDLNGAFAGEPV 61 RIIP +D++DGQ V KG +N + AK++AE+GA+ + D+ + G V Sbjct: 5 RIIPCLDVRDGQVV---KGVQFRNHEIIGDIVPLAKRYAEEGADELVFYDITASSDGRVV 61 Query: 62 NADAIAAIRKAITIPMQLGGGIRTLETLQKLFNLGVDFAILGSVAARDPELVFRACEQFP 121 + ++ + + I IP + GGI++LE K+ + G D + S A DP L+ R ++F Sbjct: 62 DKSWVSRVAEVIDIPFCVAGGIKSLEDAAKILSFGADKISINSPALADPTLITRLADRFG 121 Query: 122 GR-ISVGI----DARDGKVAV------EGWAETTDLNAVDLAKKFEDAGVAEIIFTDIAR 170 + I VGI DA GK V E T +D ++ + G EI+ + + Sbjct: 122 VQCIVVGIDTWYDAETGKYHVNQYTGDESRTRVTQWETLDWVQEVQKRGAGEIVLNMMNQ 181 Query: 171 DGTLTGPNVAATRLMAESATIPVIASGGVSCL 202 DG G ++ + + E +P+IASGG + Sbjct: 182 DGVRNGYDLEQLKKVREVCHVPLIASGGAGTM 213 Score = 23.9 bits (50), Expect = 0.003 Identities = 19/92 (20%), Positives = 40/92 (43%), Gaps = 1/92 (1%) Query: 15 VRLFKGDMDQNTVYSDNPGETAKQWAEQGAERMHVVDLNGAFAGEPVNADAIAAIRKAIT 74 V + GD + V + ++ ++GA + + +N + + + +R+ Sbjct: 142 VNQYTGDESRTRVTQWETLDWVQEVQKRGAGEIVLNMMNQDGVRNGYDLEQLKKVREVCH 201 Query: 75 IPMQLGGGIRTLETLQKLF-NLGVDFAILGSV 105 +P+ GG T+E + F + VD A+ SV Sbjct: 202 VPLIASGGAGTMEHFLEAFRDADVDGALAASV 233 Lambda K H 0.318 0.136 0.396 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: 180 Number of extensions: 11 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: 249 Length of database: 258 Length adjustment: 24 Effective length of query: 225 Effective length of database: 234 Effective search space: 52650 Effective search space used: 52650 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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