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 RR42_RS18885 RR42_RS18885 imidazole glycerol phosphate synthase
Query= curated2:Q3Z6V7 (237 letters) >FitnessBrowser__Cup4G11:RR42_RS18885 Length = 256 Score = 129 bits (324), Expect = 5e-35 Identities = 78/231 (33%), Positives = 125/231 (54%), Gaps = 13/231 (5%) Query: 3 IIPAIDILGGRCVRLLQGDYAQETVYSPDPVGTAMRWQSLGAPRLHVVDLDGAADGESVN 62 IIP +D+ GR V+ G E + DPV A R+ GA + +D+ +DG + Sbjct: 6 IIPCLDVTNGRVVK---GVNFVELRDAGDPVEIARRYDEQGADEITFLDITATSDGRDLI 62 Query: 63 FELIREIANSALIPVEVGGGIRSMDTVKKLLTAGVDRVILGTVAVENPELVREICARY-A 121 +I +A+ IP+ VGGG+R+++ V++LL AG D++ + + A+ NP+LV + ARY + Sbjct: 63 LHIIEAVASQVFIPLTVGGGVRAVEDVRRLLNAGADKISVNSSAIANPQLVSDATARYGS 122 Query: 122 DSVAVSIDARNG---------KVATRGWVNSTEVDALELARSMKKLGVKRFIYTDISRDG 172 + V+IDA+ +V T G +T +DA+ AR M G + T + RDG Sbjct: 123 QCIVVAIDAKRSSAPGEPARWEVFTHGGRKATGLDAVAWAREMAARGAGELLLTSMDRDG 182 Query: 173 TLSEPNFAAIRDLISAINMPVIASGGVSSLSHLRLLKDIGAEGAIVGKAIY 223 T S + R + A+++PVIASGGV SL L +G A++ +I+ Sbjct: 183 TKSGFDLELTRAVSDAVSVPVIASGGVGSLKDLADGIKLGHADAVLAASIF 233 Lambda K H 0.318 0.136 0.384 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: 189 Number of extensions: 12 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: 237 Length of database: 256 Length adjustment: 24 Effective length of query: 213 Effective length of database: 232 Effective search space: 49416 Effective search space used: 49416 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