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 Ga0059261_1048 Ga0059261_1048 imidazoleglycerol phosphate synthase, cyclase subunit
Query= curated2:P9WMM4 (244 letters) >FitnessBrowser__Korea:Ga0059261_1048 Length = 255 Score = 84.3 bits (207), Expect = 2e-21 Identities = 75/245 (30%), Positives = 112/245 (45%), Gaps = 36/245 (14%) Query: 5 LLPAVDVVEGRAVRLVQ----GKAGSQTEYGSAVDAALGWQRDGAEWIHLVDLDAAF-GR 59 ++P +DV GR V+ V AG E A DAA GA+ + +D+ A+ R Sbjct: 7 VIPCLDVANGRVVKGVNFVNLRDAGDPVEQARAYDAA------GADELCFLDITASHEAR 60 Query: 60 GSNHELLAEVVGKLDVQVELSGGIRDDESLAAALATGCARVNVGTAALENPQWCARVIGE 119 G+ +++ + + + GG+R E A L G +V V +AA+ P+ + + Sbjct: 61 GTIIDVVRRTAEVCFMPLTVGGGVRSAEDARALLLAGADKVAVNSAAVTRPEVVSEIAER 120 Query: 120 HGDQVAVGLDVQIIDGEHRLRGRGWE--TDGG------DLWDVLERLDSEGCSRFVVTDI 171 G Q V +D GR WE T GG D + L G ++T + Sbjct: 121 FGSQCIVAS----VDARRVADGR-WEVFTHGGRKPTGIDAVEHALHLAKLGAGELLLTSM 175 Query: 172 TKDGTLGGPNLDLLAGVADRTDAPVIASGGVSSLDDLRA-----------IATLTHRGVE 220 +DGT G +LDL+ +ADR PV+ASGGV +LD L A A++ H G E Sbjct: 176 DRDGTRDGYDLDLIRTIADRVRVPVVASGGVGNLDHLVAGIRDGHASAVLAASIFHFG-E 234 Query: 221 GAIVG 225 +IVG Sbjct: 235 ASIVG 239 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: 210 Number of extensions: 14 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: 244 Length of database: 255 Length adjustment: 24 Effective length of query: 220 Effective length of database: 231 Effective search space: 50820 Effective search space used: 50820 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