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_086508673.1 BZY95_RS03890 imidazole glycerol phosphate synthase subunit HisF
Query= curated2:A0B7W4 (242 letters) >NCBI__GCF_002151265.1:WP_086508673.1 Length = 257 Score = 129 bits (324), Expect = 6e-35 Identities = 80/233 (34%), Positives = 129/233 (55%), Gaps = 16/233 (6%) Query: 5 IFPAVDLRGGRCVQLVQGVPGSEVVSLDDPLVQAVRWADMGADHLHIIDLDGAIEGTRLN 64 I P +D+ GR +V+GV + DP+ A R+ GAD + +D+ + E Sbjct: 7 IIPCLDVDAGR---VVKGVNFIGIRDAGDPVEIAQRYNLQGADEITFLDITASHEDRDTT 63 Query: 65 APILRRIVGELEVFVQVGGGIRSRSDVAEVLDTGVDRVILGTMALRDPPVVKELAEEYGP 124 ++ RI GE+ + + VGGGIR+ D+ +L+ G D+V + T A+ +P V+E AE +G Sbjct: 64 VEMVERIAGEVFIPLTVGGGIRTCDDIRTMLNAGADKVSINTAAVTNPDFVREAAERFGS 123 Query: 125 DRIMVALDVRDGRVTSEG----WQ-------RTLEFDAIELGIVFESFGAGSILFTNIDT 173 I+VA+D + RV++EG W+ R DA+E +GAG +L T++D Sbjct: 124 QCIVVAIDAK--RVSTEGETPRWEIFTHGGRRPTGLDAVEWAKKMVEYGAGELLLTSMDR 181 Query: 174 EGQQRGVDPEPTRELVEAVSIPVIAAGGVSSLDDIKLLSDAGAAGAVIGTAIY 226 +G + G D TR + +AV++PVIA+GGV +LD + G A AV+ +I+ Sbjct: 182 DGTKAGFDLGVTRAISDAVTVPVIASGGVGNLDHLVAGVLEGGADAVLAASIF 234 Score = 49.7 bits (117), Expect = 6e-11 Identities = 37/119 (31%), Positives = 53/119 (44%), Gaps = 12/119 (10%) Query: 126 RIMVALDVRDGRVTSEGWQRTLEF-------DAIELGIVFESFGAGSILFTNIDTEGQQR 178 RI+ LDV GRV + + F D +E+ + GA I F +I + R Sbjct: 6 RIIPCLDVDAGRVV-----KGVNFIGIRDAGDPVEIAQRYNLQGADEITFLDITASHEDR 60 Query: 179 GVDPEPTRELVEAVSIPVIAAGGVSSLDDIKLLSDAGAAGAVIGTAIYTGTLNLREALE 237 E + V IP+ GG+ + DDI+ + +AGA I TA T +REA E Sbjct: 61 DTTVEMVERIAGEVFIPLTVGGGIRTCDDIRTMLNAGADKVSINTAAVTNPDFVREAAE 119 Lambda K H 0.319 0.140 0.400 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: 195 Number of extensions: 13 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: 242 Length of database: 257 Length adjustment: 24 Effective length of query: 218 Effective length of database: 233 Effective search space: 50794 Effective search space used: 50794 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: 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