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_013076129.1 BTUS_RS10910 imidazole glycerol phosphate synthase subunit HisF
Query= curated2:Q18DL2 (245 letters) >NCBI__GCF_000092905.1:WP_013076129.1 Length = 253 Score = 114 bits (286), Expect = 1e-30 Identities = 78/235 (33%), Positives = 124/235 (52%), Gaps = 14/235 (5%) Query: 10 VIPAVDMQDGDVVQLVQGERGTETRYGDPVVAAKQWVEAGAKTLHLVDLDGAFEGDRMNA 69 ++P D+++G VV+ V E GDPV A+ + E+GA L L+D+ + EG A Sbjct: 6 IVPCFDVKNGRVVKNVSFLTN-ERDAGDPVELARYYDESGADELVLLDISASVEG---RA 61 Query: 70 TAVDAIIDA---VDIPVQLGGGIRTANDAASLLDRGVNRVILGTAAVENPDLVAELAESY 126 T VD + V IP+ +GGGI + +D LL G ++V + T AV++P LV E A+ Y Sbjct: 62 TMVDVVARTAAEVFIPLTVGGGITSVDDIRVLLKAGADKVSINTGAVKHPQLVLEAAKRY 121 Query: 127 PGR-IIVSLDA------ADGEVVVSGWTESTGIDPAVAAARFADYGACGILFTDVDVEGK 179 + I+V++D D EV+++G TG+ A + + GA IL T D +G+ Sbjct: 122 GQQCIVVAIDGKYDGQKGDWEVLINGGRTRTGLSAVEWAKKMENLGAGEILLTSFDQDGR 181 Query: 180 LAGIQSSVTARVIDAVDIPVIASGGVASLDDIQTLHTTGAAATVVGTALYENKFT 234 G + T + ++V+IPVIASGG + + T G A + +++ K T Sbjct: 182 KDGYDLTFTRVISESVNIPVIASGGAGKKEHFYEVFTKGKADAALAASIFHFKET 236 Score = 43.5 bits (101), Expect = 4e-09 Identities = 33/113 (29%), Positives = 50/113 (44%), Gaps = 3/113 (2%) Query: 129 RIIVSLDAADGEVV--VSGWT-ESTGIDPAVAAARFADYGACGILFTDVDVEGKLAGIQS 185 RI+ D +G VV VS T E DP A + + GA ++ D+ + Sbjct: 5 RIVPCFDVKNGRVVKNVSFLTNERDAGDPVELARYYDESGADELVLLDISASVEGRATMV 64 Query: 186 SVTARVIDAVDIPVIASGGVASLDDIQTLHTTGAAATVVGTALYENKFTLADA 238 V AR V IP+ GG+ S+DDI+ L GA + T ++ + +A Sbjct: 65 DVVARTAAEVFIPLTVGGGITSVDDIRVLLKAGADKVSINTGAVKHPQLVLEA 117 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: 144 Number of extensions: 7 Number of successful extensions: 3 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: 253 Length adjustment: 24 Effective length of query: 221 Effective length of database: 229 Effective search space: 50609 Effective search space used: 50609 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 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