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 WP_013420003.1 RVAN_RS12085 imidazole glycerol phosphate synthase subunit HisF
Query= curated2:Q3Z6V7 (237 letters) >NCBI__GCF_000166055.1:WP_013420003.1 Length = 262 Score = 122 bits (305), Expect = 9e-33 Identities = 76/245 (31%), Positives = 124/245 (50%), Gaps = 16/245 (6%) Query: 1 MEIIPAIDILGGRCVRLLQGDYAQETVYSPDPVGTAMRWQSLGAPRLHVVDLDGAADGES 60 + IIP +D+ GR V+ G + + DPV A + GA L +D+ + + Sbjct: 4 VRIIPCLDVKDGRVVK---GVNFVDLRDAGDPVEAAAAYDEAGADELCFLDITASHEKRG 60 Query: 61 VNFELIREIANSALIPVEVGGGIRSMDTVKKLLTAGVDRVILGTVAVENPELVREICARY 120 +++ A +P+ VGGG+R++D V+ LL AG D+V + T AV N V E ++ Sbjct: 61 TILDVVARTAERCFMPLTVGGGVRTLDDVRTLLRAGADKVSINTAAVTNRAFVGEAAEKF 120 Query: 121 ADS-VAVSIDAR-----------NGKVATRGWVNSTEVDALELARSMKKLGVKRFIYTDI 168 + + V+IDA+ + ++ T G N T +DA++ A+ + LG + T + Sbjct: 121 GNQCIVVAIDAKRVDDEGDGRGAHWEIFTHGGRNRTGIDAIDFAKDVVALGAGEILLTSM 180 Query: 169 SRDGTLSEPNFAAIRDLISAINMPVIASGGVSSLSHL-RLLKDIGAEGAIVGKAIYTGDL 227 RDGT S + A R + A+ +PVIASGGV +L HL ++D GA + + GD Sbjct: 181 DRDGTRSGFDLALTRAISDAVQVPVIASGGVGNLDHLVEGIRDGGATAVLAASIFHFGDY 240 Query: 228 NLKRA 232 + A Sbjct: 241 TIGEA 245 Score = 30.4 bits (67), Expect = 4e-05 Identities = 29/116 (25%), Positives = 49/116 (42%), Gaps = 14/116 (12%) Query: 128 IDARNGKVATRGWVNSTEV----DALELARSMKKLGVKRFIYTDISRDGTLSEPNFAAIR 183 +D ++G+V VN ++ D +E A + + G + DI T S I Sbjct: 10 LDVKDGRVVKG--VNFVDLRDAGDPVEAAAAYDEAGADELCFLDI----TASHEKRGTIL 63 Query: 184 DLISAIN----MPVIASGGVSSLSHLRLLKDIGAEGAIVGKAIYTGDLNLKRAFEE 235 D+++ MP+ GGV +L +R L GA+ + A T + A E+ Sbjct: 64 DVVARTAERCFMPLTVGGGVRTLDDVRTLLRAGADKVSINTAAVTNRAFVGEAAEK 119 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: 183 Number of extensions: 15 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: 237 Length of database: 262 Length adjustment: 24 Effective length of query: 213 Effective length of database: 238 Effective search space: 50694 Effective search space used: 50694 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 10 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