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_011024313.1 MA_RS23175 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase
Query= curated2:A2SQR0 (236 letters) >NCBI__GCF_000007345.1:WP_011024313.1 Length = 245 Score = 57.0 bits (136), Expect = 3e-13 Identities = 49/169 (28%), Positives = 81/169 (47%), Gaps = 6/169 (3%) Query: 61 NAEMIREVVEKTDVFVQVGGGIRSLEDARGWLNCGVARIILSTFATREPAVIRTLSKEFG 120 NAE+IREV K D + G + L D L+ +L T T + +VIR Sbjct: 70 NAEVIREVSLKADTMLDFG--VSCLGDVDRALSIA-GTAVLGT-ETGKLSVIRDAVARCP 125 Query: 121 SERIMAGVDARRGEIAVSGWQELAGDFIVWAQKFEELGAGSLLYTNVDVEGQQAGIDIEP 180 RI +D + G++ E+ D + EL L++ ++D G +G D E Sbjct: 126 G-RISVSIDVKYGKLLKQD-PEIPEDPFEIVKLLNELPLKDLIFLDLDRVGTASGFDPEF 183 Query: 181 VQKLLDAVDIPVIVAGGVTTSQDVTALKQLGASGCVLGSALYSGRITLK 229 + KL + V++AGGV +D+ L +LG G ++ +A++SG + L+ Sbjct: 184 LHKLAETSIHDVLLAGGVRGMEDLFTLDRLGIKGALVATAIHSGEVPLE 232 Score = 27.3 bits (59), Expect = 3e-04 Identities = 16/59 (27%), Positives = 31/59 (52%) Query: 45 NLHVVNLDGAFTASTTNAEMIREVVEKTDVFVQVGGGIRSLEDARGWLNCGVARIILST 103 +L ++LD TAS + E + ++ E + V + GG+R +ED G+ +++T Sbjct: 164 DLIFLDLDRVGTASGFDPEFLHKLAETSIHDVLLAGGVRGMEDLFTLDRLGIKGALVAT 222 Lambda K H 0.318 0.135 0.387 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: 117 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: 236 Length of database: 245 Length adjustment: 23 Effective length of query: 213 Effective length of database: 222 Effective search space: 47286 Effective search space used: 47286 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