Align 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; EC 5.3.1.16; Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (uncharacterized)
to candidate AO356_03380 AO356_03380 glycosyl amidation-associated protein WbuZ
Query= curated2:Q8PWS2 (246 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_03380 Length = 253 Score = 107 bits (268), Expect = 2e-28 Identities = 64/202 (31%), Positives = 110/202 (54%), Gaps = 9/202 (4%) Query: 31 IDDPLAVALDWVSKGAKTLHLVDLDGAIEGERKNSPIIEKIVNTCKEKGVSIQVGGGIRS 90 + DP+ + K L L+D++ +I G + ++ ++ C + I GGGIR+ Sbjct: 29 VGDPVNAIRIFNEKEVDELVLLDIEASILGREPDYELLAEVAGECF---MPICYGGGIRT 85 Query: 91 FEDAASLLEIGVSRIILGTAALQNPELVKQLSSSFGSSHVNVALDAKN---GKISI--KG 145 E A + +GV +I L TAAL + EL+++++ FGS V ++D K G+ S+ + Sbjct: 86 LEHAQRVFALGVEKIALNTAALADVELLRKIADQFGSQSVVCSIDCKKSLLGRYSVYSQS 145 Query: 146 WTEECAQTPVEMGRKFEELGAGSLLFTNIDTEGLMQGVNPVPTKELVESVSIPVIASGGV 205 T++ +PVE ++ E+ GAG + +ID +G MQG + K +V V IPV+A GG Sbjct: 146 GTKDTKVSPVEWAKRVEDAGAGEIFLNSIDRDGTMQGFDIPLIKSVVAGVHIPVVACGGA 205 Query: 206 STLEDI-KTLKKTGAAGVVVGS 226 ++ D+ + +K G + V GS Sbjct: 206 GSIADLNEPFEKAGVSAVAAGS 227 Score = 25.0 bits (53), Expect = 0.001 Identities = 17/74 (22%), Positives = 31/74 (41%) Query: 154 PVEMGRKFEELGAGSLLFTNIDTEGLMQGVNPVPTKELVESVSIPVIASGGVSTLEDIKT 213 PV R F E L+ +I+ L + + E+ +P+ GG+ TLE + Sbjct: 32 PVNAIRIFNEKEVDELVLLDIEASILGREPDYELLAEVAGECFMPICYGGGIRTLEHAQR 91 Query: 214 LKKTGAAGVVVGSA 227 + G + + +A Sbjct: 92 VFALGVEKIALNTA 105 Lambda K H 0.314 0.134 0.373 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: 160 Number of extensions: 9 Number of successful extensions: 4 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: 246 Length of database: 253 Length adjustment: 24 Effective length of query: 222 Effective length of database: 229 Effective search space: 50838 Effective search space used: 50838 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: 42 (21.9 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