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_007474496.1 CMTB2_RS05035 imidazole glycerol phosphate synthase subunit HisF
Query= curated2:Q8PWS2 (246 letters) >NCBI__GCF_000170735.1:WP_007474496.1 Length = 253 Score = 115 bits (289), Expect = 6e-31 Identities = 72/223 (32%), Positives = 121/223 (54%), Gaps = 13/223 (5%) Query: 5 VIPAVDMRGGKCVQLVQGVPGSEIVSIDDPLAVALDWVSKGAKTLHLVDLDGAIEGERKN 64 +IP +D++ G+ +V+GV + DP+ A+ + +GA L +D+ + E ERK Sbjct: 8 IIPCLDVKDGR---VVKGVNFVGLKDAGDPVEAAIRYNEEGADELTFLDITASYE-ERK- 62 Query: 65 SPIIEKIVNTCKEKGVSIQVGGGIRSFEDAASLLEIGVSRIILGTAALQNPELVKQLSSS 124 PI++ + KE + + VGGGI S ++ LL +G ++ + +AA++ PE + + S Sbjct: 63 -PIVDIVKEVAKEVFIPLTVGGGINSLKNIYDLLNVGCDKVSINSAAVKRPEFINEASKR 121 Query: 125 FGSSHVNVALDAK-----NGKISIKGWTEECAQTPVEMGRKFEELGAGSLLFTNIDTEGL 179 FGSS + VA+D K + IKG E+ ++ ++ + GAG +L T++DT+G Sbjct: 122 FGSSTIVVAIDVKKITPNKWNVFIKGGREDTGLDAIKWAKEVVDRGAGEILLTSMDTDGT 181 Query: 180 MQGVNPVPTKELVESVSIPVIASGGVSTLEDIKT--LKKTGAA 220 G + T+ + V +PVIASGG +E K L K AA Sbjct: 182 KNGFDIEITEIISSLVHVPVIASGGAGEVEHFKEAFLHKADAA 224 Score = 40.4 bits (93), Expect = 3e-08 Identities = 31/99 (31%), Positives = 50/99 (50%), Gaps = 8/99 (8%) Query: 134 LDAKNGKISIKGWTE---ECAQTPVEMGRKFEELGAGSLLFTNIDTEGLMQGVNPVP--T 188 LD K+G++ +KG + A PVE ++ E GA L F +D + P+ Sbjct: 12 LDVKDGRV-VKGVNFVGLKDAGDPVEAAIRYNEEGADELTF--LDITASYEERKPIVDIV 68 Query: 189 KELVESVSIPVIASGGVSTLEDIKTLKKTGAAGVVVGSA 227 KE+ + V IP+ GG+++L++I L G V + SA Sbjct: 69 KEVAKEVFIPLTVGGGINSLKNIYDLLNVGCDKVSINSA 107 Lambda K H 0.314 0.134 0.373 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: 162 Number of extensions: 11 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: 246 Length of database: 253 Length adjustment: 24 Effective length of query: 222 Effective length of database: 229 Effective search space: 50838 Effective search space used: 50838 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: 42 (21.9 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