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_012336409.1 M446_RS32885 imidazole glycerol phosphate synthase subunit HisF
Query= curated2:Q18DL2 (245 letters) >NCBI__GCF_000019365.1:WP_012336409.1 Length = 258 Score = 128 bits (321), Expect = 1e-34 Identities = 85/240 (35%), Positives = 128/240 (53%), Gaps = 13/240 (5%) Query: 10 VIPAVDMQDGDVVQLVQGERGTETRYGDPVVAAKQWVEAGAKTLHLVDLDGAFEGDRMNA 69 VIP +D++DG VV+ VQ + GDPV AAK + AGA L +D+ + E + Sbjct: 6 VIPCLDVKDGRVVKGVQFLALRDA--GDPVEAAKAYDAAGADELCFLDITASHEARGILL 63 Query: 70 TAVDAIIDAVDIPVQLGGGIRTANDAASLLDRGVNRVILGTAAVENPDLVAELAESYPGR 129 V +A +P+ +GGG+R+ D +LL G ++V + TAAV NPD VAE AE + + Sbjct: 64 DVVQRTAEACFMPLTVGGGVRSVEDIRALLLAGADKVSINTAAVNNPDFVAEAAEKFGNQ 123 Query: 130 -IIVSLD---------AADGEVVVSGWTESTGIDPAVAAARFADYGACGILFTDVDVEGK 179 I+V++D A E+ G +TG+D A GA +L T +D +G Sbjct: 124 CIVVAIDAKRVSGPGEAPRWEIFTHGGRRATGLDAITFARTVTARGAGELLVTSMDRDGM 183 Query: 180 LAGIQSSVTARVIDAVDIPVIASGGVASLDDIQTLHTTGAAATVVGTALYE-NKFTLADA 238 +G +T + DAV +PVIASGGV LDD+ G A+ V+ +++ + T+A A Sbjct: 184 RSGYDLGLTRAIADAVSVPVIASGGVGGLDDLVAGVAEGHASAVLAASIFHFGEATVAQA 243 Score = 55.1 bits (131), Expect = 1e-12 Identities = 38/114 (33%), Positives = 52/114 (45%), Gaps = 2/114 (1%) Query: 129 RIIVSLDAADGEVV--VSGWTESTGIDPAVAAARFADYGACGILFTDVDVEGKLAGIQSS 186 R+I LD DG VV V DP AA + GA + F D+ + GI Sbjct: 5 RVIPCLDVKDGRVVKGVQFLALRDAGDPVEAAKAYDAAGADELCFLDITASHEARGILLD 64 Query: 187 VTARVIDAVDIPVIASGGVASLDDIQTLHTTGAAATVVGTALYENKFTLADAME 240 V R +A +P+ GGV S++DI+ L GA + TA N +A+A E Sbjct: 65 VVQRTAEACFMPLTVGGGVRSVEDIRALLLAGADKVSINTAAVNNPDFVAEAAE 118 Lambda K H 0.316 0.133 0.375 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: 153 Number of extensions: 8 Number of successful extensions: 4 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: 245 Length of database: 258 Length adjustment: 24 Effective length of query: 221 Effective length of database: 234 Effective search space: 51714 Effective search space used: 51714 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 (21.6 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