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 201226 SO2069 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (NCBI ptt file)
Query= curated2:P9WMM4 (244 letters) >FitnessBrowser__MR1:201226 Length = 245 Score = 131 bits (329), Expect = 1e-35 Identities = 80/242 (33%), Positives = 134/242 (55%), Gaps = 9/242 (3%) Query: 4 ILLPAVDVVEGRAVRLVQGKAGSQTEYGSAVDAAL-GWQRDGAEWIHLVDLDAAFGRGSN 62 +++PA+D+++G+ VRL QG G QT + + A L +Q A W+H+VDL A Sbjct: 1 MIIPAIDLIDGKVVRLYQGDYGQQTTFDLSPLAQLQSYQAQDASWLHIVDLTGAKDPAKR 60 Query: 63 H-ELLAEVVGKLDVQVELSGGIRDDESLAAALATGCARVNVGTAALENPQWCARVIGEHG 121 L+A + L +++ GGIR +E +A L+ G RV +G+ A++ P+ + G Sbjct: 61 QTALIAALTAGLSANIQVGGGIRTEEQVAELLSLGVKRVVIGSLAVKEPELVKGWFNKFG 120 Query: 122 DQ-VAVGLDVQII-DGEHRLRGRGWETDGG-DLWDVLERLDSEGCSRFVVTDITKDGTLG 178 ++ + + LD+ I GE + GW+ GG +L ++E G +VTDI++DGTL Sbjct: 121 NEAICLALDINITPSGEKIVAVSGWQNGGGKNLESIVEDFSQVGLKHALVTDISRDGTLT 180 Query: 179 GPNLDLLAGVADR-TDAPVIASGGVSSLDDLRAIATLTHRGVEGAIVGKALYARRFTLPQ 237 G N +L ++ R + ASGG++SL+D +A + G G I+GKAL +F + + Sbjct: 181 GANTELYCELSSRYPNIAWQASGGIASLED---VAAVRDSGAAGIIIGKALLINQFNVAE 237 Query: 238 AL 239 A+ Sbjct: 238 AI 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: 182 Number of extensions: 17 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: 245 Length adjustment: 24 Effective length of query: 220 Effective length of database: 221 Effective search space: 48620 Effective search space used: 48620 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