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_017550017.1 C792_RS0113620 imidazole glycerol phosphate synthase subunit HisF
Query= curated2:A3CTR9 (239 letters) >NCBI__GCF_000330705.1:WP_017550017.1 Length = 254 Score = 101 bits (251), Expect = 2e-26 Identities = 69/227 (30%), Positives = 111/227 (48%), Gaps = 9/227 (3%) Query: 3 IYPAVDILDGRCVQLVQGRPEAATVYGDPAAWAHRWLDEGADGLHVVNLDGAFGRARKNA 62 I P +D+ DGR V+ V GDP A R+ +EGAD L +++ Sbjct: 6 IIPCLDVKDGRVVKGVNFI--GLRDIGDPVELAKRYNEEGADELVFLDISKTQEGHDLMI 63 Query: 63 DLIRAFTRETETFTELGGGIRSVEDAAGWLDAGVDRVIVSTQAVREPEMIRTLAEEFGGE 122 D+IR +E +GGG+ SV D L AG D+V +++ A+R+P +I+T A+ FG + Sbjct: 64 DVIRDTAKELFIPLTIGGGVSSVGDIRQLLGAGADKVSINSAALRDPGLIKTAADVFGSQ 123 Query: 123 RVMAGIDARAGEVMIE------GWERPAG-SYLSWAERFESLGAGSLLYTNVDVEGLQQG 175 + ID + V + G + G W E+ +LGAG LL T++D +G++QG Sbjct: 124 CICIAIDVKYDAVKADYFVFTHGGSKDTGIRAFEWIEQCAALGAGELLITSMDHDGVKQG 183 Query: 176 IAIEPVTELLARVKVPVVVSGGISSPGDVAALRDAGAAGAVLGSALY 222 + + V +P++ SGG PG L A L ++++ Sbjct: 184 FNTVFLKQAKELVDIPIIASGGAGDPGHFIELFRETDVSAGLAASIF 230 Lambda K H 0.317 0.135 0.397 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: 123 Number of extensions: 7 Number of successful extensions: 3 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: 239 Length of database: 254 Length adjustment: 24 Effective length of query: 215 Effective length of database: 230 Effective search space: 49450 Effective search space used: 49450 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 Jul 26 2024. The underlying query database was built on Jul 25 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