Align Phosphoribosyl isomerase A; 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; EC 5.3.1.16; N-(5'-phosphoribosyl)anthranilate isomerase; PRAI; EC 5.3.1.24; Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (uncharacterized)
to candidate WP_041100145.1 SUTH_RS14135 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= curated2:P60583 (243 letters) >NCBI__GCF_000828635.1:WP_041100145.1 Length = 250 Score = 142 bits (358), Expect = 6e-39 Identities = 86/243 (35%), Positives = 137/243 (56%), Gaps = 9/243 (3%) Query: 2 LILLPAVDVVDGRAVRLVQGKAGSETEYGSALDA-ALGWQRDGAEWIHLVDLDAAF-GRG 59 ++L+PA+D+ DG VRL QG T + A A W GA +HLVDL+ AF G+ Sbjct: 1 MLLIPAIDLKDGHCVRLKQGAMEDATVFSEDPAAMARHWIDQGARRLHLVDLNGAFAGKP 60 Query: 60 SNRELLAEVVGKL--DVRVELSGGIRDDDSLAAALATGCARVNLGTAALENPQWCARAIG 117 N + ++ ++ ++ V+L GGIRD D++ L G V +GTAA++NP + A G Sbjct: 61 KNEAAIKAILKEVGDEIPVQLGGGIRDLDTIERCLDDGITYVIIGTAAVKNPGFLHDACG 120 Query: 118 EHGDKVAVGLDVQIIDGQHRLRGRGW-ETDGGDLWEVLERLERQGCSRYVVTDVTKDGTL 176 + VGLD + DG ++ GW + G D+ ++ ++ E G + TD+ +DG L Sbjct: 121 AFPGHIIVGLDAK--DG--KVAVDGWSKMTGHDVVDLAKKFEDYGVEAVIYTDIGRDGML 176 Query: 177 GGPNLDLLGAVADRTDAPVIASGGVSSLDDLRAIATLTGRGVEGAIVGKALYAGRFTLPQ 236 G N++ +A PVIASGG++S+ D++A+ + G G+ GAI G+A+Y G+ + Sbjct: 177 SGVNIEATVKLAQALRIPVIASGGIASVKDVKALCAVQGEGISGAITGRAIYEGKLDFKK 236 Query: 237 ALA 239 A A Sbjct: 237 AQA 239 Lambda K H 0.318 0.138 0.407 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: 207 Number of extensions: 12 Number of successful extensions: 4 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: 243 Length of database: 250 Length adjustment: 24 Effective length of query: 219 Effective length of database: 226 Effective search space: 49494 Effective search space used: 49494 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 09 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