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 N515DRAFT_2932 N515DRAFT_2932 cyclase
Query= curated2:Q2JK82 (261 letters) >FitnessBrowser__Dyella79:N515DRAFT_2932 Length = 256 Score = 101 bits (251), Expect = 2e-26 Identities = 76/250 (30%), Positives = 126/250 (50%), Gaps = 18/250 (7%) Query: 10 VIPAIDLLQGRAVRLYQGDYAQAEQVADDPIQQAEAWAAQGAPRLHVVDLDGAKSGDPVN 69 +IP +D+ G+ V+ G + V + ++ A + +GA L D+ + G V+ Sbjct: 6 IIPCLDVRDGKVVK---GVRFRDHVVMGEIVELALRYRDEGADELVFYDITASPEGRSVD 62 Query: 70 LPIIERIVRSLAIPVQVGGGIRSLERARQLLDLGVDRVIVGTLAVEDPDTLEAMTQAFPG 129 +ER+ R++ IP V GGIRS+E AR++L G D++ V + A+E P + + AF Sbjct: 63 RGWVERVARAIDIPFCVAGGIRSVEDAREVLHAGADKISVNSPALERPALIGELAAAFGV 122 Query: 130 R-VWVGIDA---RQGQVATRGWLSTTPLRAPELVQR-------VQAQGAAGIIYTDISRD 178 + V VG+D+ G+ R + + P + L +R Q GA I+ + D Sbjct: 123 QCVVVGVDSLRDADGEWRVRQY-TGDPTKTQALARRTLDWIDEAQRLGAGEIVLNCMGSD 181 Query: 179 GTLAGPNLEQLRQILAVSQVPVIASGGIGSLTDLLALLSLPRLTGAILGKALYSGAI--- 235 G G +LEQL A+ +VP++ASGG G+ ++ + GA+ +SGAI Sbjct: 182 GVREGYDLEQLHAARALCRVPLVASGGAGAPEHFRDAFAVADVDGALAASVFHSGAIAIP 241 Query: 236 SLQEALRAVG 245 SL++ LR G Sbjct: 242 SLKQYLRRAG 251 Lambda K H 0.319 0.137 0.400 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: 196 Number of extensions: 13 Number of successful extensions: 2 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: 261 Length of database: 256 Length adjustment: 24 Effective length of query: 237 Effective length of database: 232 Effective search space: 54984 Effective search space used: 54984 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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