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 CA265_RS03615 CA265_RS03615 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino]imidazole-4- carboxamide isomerase
Query= curated2:P9WMM4 (244 letters) >FitnessBrowser__Pedo557:CA265_RS03615 Length = 249 Score = 132 bits (331), Expect = 8e-36 Identities = 80/244 (32%), Positives = 141/244 (57%), Gaps = 16/244 (6%) Query: 3 LILLPAVDVVEGRAVRLVQGKAGSQTEYGSAVDAALG-WQRDGAEWIHLVDLDAAFGRGS 61 + ++PA+D+++G+ VRL +G +TEY ++ + ++ +G ++IH++DL+ A G S Sbjct: 1 MYIIPAIDILDGKVVRLREGDYNQKTEYAVSIPEMIEKYRSNGTDFIHIIDLNGAKGDFS 60 Query: 62 NHELLAEVVGKLDVQVELSGGIRDDESLAAALATGCARVNVGTAALENPQWCARVI---- 117 N + L E++ K +++V+ GGIR E + L G RV VGT A+ NP + ++ Sbjct: 61 NQKTLFEIIKKTEMKVQYGGGIRTIEQVTNLLDAGIHRVIVGTQAITNPDFLPQLSEAFA 120 Query: 118 --GEHGDQVAVGLDVQIIDGEHRLRGRGW-ETDGGDLWDVLERLDSEGCSRFVVTDITKD 174 ++ +++ + +DV + ++ GW E+ L D +++ S G RF+ TDI+KD Sbjct: 121 KKDDYANRIVIAIDVL----DEVIKYSGWMESSPIKLMDYVDKCLSLGFFRFLCTDISKD 176 Query: 175 GTLGGPNLDLLAGVADRTD-APVIASGGVSSLDDLRAIATLTHRGVEGAIVGKALYARRF 233 G LGG +DL + + + +IASGGVSS+ D+ +A R V +VGKA+Y R Sbjct: 177 GKLGGAAIDLYEKLLEHSPMIKLIASGGVSSMQDIYDLAKYPIRSV---VVGKAIYEDRI 233 Query: 234 TLPQ 237 T+ + Sbjct: 234 TIEE 237 Lambda K H 0.318 0.137 0.410 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: 169 Number of extensions: 11 Number of successful extensions: 5 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: 244 Length of database: 249 Length adjustment: 24 Effective length of query: 220 Effective length of database: 225 Effective search space: 49500 Effective search space used: 49500 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