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_014026985.1 PYRFU_RS07130 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
Query= curated2:B8FP23 (250 letters) >NCBI__GCF_000223395.1:WP_014026985.1 Length = 235 Score = 151 bits (382), Expect = 1e-41 Identities = 90/236 (38%), Positives = 146/236 (61%), Gaps = 12/236 (5%) Query: 7 PAIDLKEGKAVRLLQGRMEDATVYGEQPVEVARKFKEQGADSLHVVDLDGAFAGKPVNDA 66 P++DL+ G+ V+ ++G V G P+EVA++ E+G + LHVVDLDGA AGKPVN Sbjct: 2 PSLDLEAGRVVKRVEGVKGTGLVVGS-PLEVAKRLWEKGVEWLHVVDLDGAEAGKPVNVG 60 Query: 67 VILKLIQSSGLRVQVGGGIRTLERIEELL-KLGVERVILGTVAVRNPELVEKAVQRF-EE 124 + L++ G VQ GGGIR E +E LL K+GVERV++GT+ RNP LVE V+ + + Sbjct: 61 IAESLVR-MGFHVQYGGGIRAKEHVELLLDKIGVERVVIGTLVHRNPRLVEDVVEEYGGD 119 Query: 125 AVVIGIDAKDGLVAVQGWAEKTEIKAL-DLALRMKKVGVKHLVFTDISRDGMLQGPNIQS 183 +V +DAK G+V ++GW + E K+L D+ + +GV+ +++T + R+G L G +++ Sbjct: 120 RIVAALDAKWGMVVIEGW--RKEAKSLRDMLDLVYGLGVRQILYTSVEREGKLTGADLER 177 Query: 184 TVELARLSGLQVVASGGVSRLEDLRLLQEEANRGVSLEGAIVGKALYAGAFSLAEA 239 L + + +GG++ ++D+ L E + ++ AI+G A +AG + EA Sbjct: 178 VAWLRGVWPYGLQYAGGIATIDDILGLAE-----LGVDAAILGMAFHAGLLDVVEA 228 Lambda K H 0.318 0.137 0.369 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: 205 Number of extensions: 15 Number of successful extensions: 7 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: 250 Length of database: 235 Length adjustment: 23 Effective length of query: 227 Effective length of database: 212 Effective search space: 48124 Effective search space used: 48124 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 (21.7 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