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_051955467.1 DL88_RS01890 imidazole glycerol phosphate synthase subunit HisF
Query= curated2:Q18DL2 (245 letters) >NCBI__GCF_000745425.1:WP_051955467.1 Length = 265 Score = 120 bits (301), Expect = 3e-32 Identities = 85/239 (35%), Positives = 131/239 (54%), Gaps = 11/239 (4%) Query: 10 VIPAVDMQDGDVVQLVQGERGTETR-YGDPVVAAKQWVEAGAKTLHLVDLDGAFEGDRMN 68 VIP +D++DG VV+ G + R GDPV A + AGA L +D+ + E + Sbjct: 6 VIPCLDVKDGRVVK---GVNFVDLRDAGDPVQCAMAYDAAGADELCFLDITASHEDRSIL 62 Query: 69 ATAVDAIIDAVDIPVQLGGGIRTANDAASLLDRGVNRVILGTAAVENPDLVAELAESYPG 128 V+ +A +P+ +GGG+RT +D LL G ++V + +AAV + D V AE + Sbjct: 63 FDVVERTAEACFMPLTVGGGVRTEDDIRKLLLAGADKVSIMSAAVTDRDFVRRAAEKFGS 122 Query: 129 R-IIVSLDA-ADG----EVVVSGWTESTGIDPAVAAARFADYGACGILFTDVDVEGKLAG 182 + ++V++DA A G EV G + TGID A A+ GA IL T +D +G AG Sbjct: 123 QCVVVAIDAKATGPGRWEVFTHGGRKPTGIDAIAYARDVAERGAGEILLTSMDRDGTKAG 182 Query: 183 IQSSVTARVIDAVDIPVIASGGVASLDD-IQTLHTTGAAATVVGTALYENKFTLADAME 240 ++T V ++V IPVIASGGV +LD ++ + GA A + + + FT+A+A + Sbjct: 183 FDLALTRAVAESVPIPVIASGGVGTLDHLVEGIAQGGADAVLAASIFHFGTFTIAEAKD 241 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: 157 Number of extensions: 9 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: 245 Length of database: 265 Length adjustment: 24 Effective length of query: 221 Effective length of database: 241 Effective search space: 53261 Effective search space used: 53261 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: 47 (22.7 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