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 7024671 Shewana3_1849 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase (RefSeq)
Query= curated2:P9WMM4 (244 letters) >FitnessBrowser__ANA3:7024671 Length = 245 Score = 127 bits (319), Expect = 2e-34 Identities = 81/244 (33%), Positives = 135/244 (55%), Gaps = 13/244 (5%) Query: 4 ILLPAVDVVEGRAVRLVQGKAGSQTEYGSAVDAAL-GWQRDGAEWIHLVDLDAAFGRGSN 62 +++PA+D+++G+ VRL QG G QT + + L +Q GA W+H+VDL A Sbjct: 1 MIIPAIDLIDGQIVRLYQGDYGQQTTFDLSPQTQLQSYQDQGASWLHIVDLTGAKEPAKR 60 Query: 63 H-ELLAEVVGKLDVQVELSGGIRDDESLAAALATGCARVNVGTAALENPQWCARVIGEHG 121 L+A++ L+ +++ GGIR +E +A L+ G RV +G+ A++ P+ + G Sbjct: 61 QTALIAKLTAGLNANIQVGGGIRTEEQVAELLSLGVKRVVIGSLAVKEPELVKGWFNKFG 120 Query: 122 DQ-VAVGLDVQI-IDGEHRLRGRGWETDGG-DLWDVLERLDSEGCSRFVVTDITKDGTLG 178 + + + LDV I +GE + GW++ GG L ++E G +VTDI +DGTL Sbjct: 121 SEAICLALDVNINQNGEKIVAVSGWQSGGGKSLESIVEDFSQVGLKHALVTDINRDGTLT 180 Query: 179 GPNLDLLAGVADRTDAPVI---ASGGVSSLDDLRAIATLTHRGVEGAIVGKALYARRFTL 235 G N L ++ + P I ASGG+++L+D +A + G G I+GKAL +F + Sbjct: 181 GANTALYRELS--SHYPHIAWQASGGIATLED---VAAVRDSGAAGIIIGKALLINQFNV 235 Query: 236 PQAL 239 +A+ Sbjct: 236 AEAI 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: 180 Number of extensions: 16 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