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_013450396.1 CALNI_RS01310 imidazole glycerol phosphate synthase subunit HisF
Query= curated2:P9WMM4 (244 letters) >NCBI__GCF_000183405.1:WP_013450396.1 Length = 253 Score = 99.4 bits (246), Expect = 6e-26 Identities = 67/213 (31%), Positives = 112/213 (52%), Gaps = 15/213 (7%) Query: 5 LLPAVDVVEGRAVRLVQGKAGSQTEYGSAVDAALGWQRDGAEWIHLVDLDAAF-GRGSNH 63 ++P +DV +GR V+ Q + + G V A + R GA+ + +D+ A+ RG Sbjct: 6 IIPCLDVKDGRVVKGTQFL--NLIDAGDPVQVAEEYDRQGADELTFLDITASHENRGIIL 63 Query: 64 ELLAEVVGKLDVQVELSGGIRDDESLAAALATGCARVNVGTAALENPQWCARVIGEHGDQ 123 +++A+ K+ + + + GGIR E + L +G +V++ TAA++NP + G Q Sbjct: 64 DVVAKTAEKVFMPLTVGGGIRTIEDIRKLLNSGADKVSINTAAVKNPDFVKDAALRFGSQ 123 Query: 124 VAVGLDVQIIDGEHRLRGRGWE--TDGG------DLWDVLERLDSEGCSRFVVTDITKDG 175 V ID + + G GWE T GG D+ + +++S G ++T + KDG Sbjct: 124 CIV----VAIDAKRKTNGSGWEVYTHGGRNPTGIDVLEWAVKMESFGAGEILLTSMDKDG 179 Query: 176 TLGGPNLDLLAGVADRTDAPVIASGGVSSLDDL 208 T G +L+L A V+D PVIASGGV + +D+ Sbjct: 180 TKDGYDLELTAAVSDAIRIPVIASGGVGTKEDI 212 Score = 40.8 bits (94), Expect = 3e-08 Identities = 20/65 (30%), Positives = 32/65 (49%) Query: 147 DGGDLWDVLERLDSEGCSRFVVTDITKDGTLGGPNLDLLAGVADRTDAPVIASGGVSSLD 206 D GD V E D +G DIT G LD++A A++ P+ GG+ +++ Sbjct: 28 DAGDPVQVAEEYDRQGADELTFLDITASHENRGIILDVVAKTAEKVFMPLTVGGGIRTIE 87 Query: 207 DLRAI 211 D+R + Sbjct: 88 DIRKL 92 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: 203 Number of extensions: 14 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: 244 Length of database: 253 Length adjustment: 24 Effective length of query: 220 Effective length of database: 229 Effective search space: 50380 Effective search space used: 50380 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