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_078717578.1 B5D49_RS10105 imidazole glycerol phosphate synthase subunit HisF
Query= curated2:A0LHK5 (256 letters) >NCBI__GCF_900167125.1:WP_078717578.1 Length = 259 Score = 106 bits (264), Expect = 5e-28 Identities = 68/220 (30%), Positives = 115/220 (52%), Gaps = 18/220 (8%) Query: 3 IFPAIDIKDGVCVRLMQGDPDRVTVYGKDPVSVAKRWEGEGAGWLHVVDLDGAFLRRPAN 62 + P +D+++G RL +G + V DPV AKR+ EGA + D+ + R Sbjct: 6 VIPCLDVRNG---RLTKGIKFKNNVDIGDPVETAKRYYEEGADEIVFYDITASSEARGIF 62 Query: 63 RQVVASIVKAVSIPVQVGGGIRNLEAIRDYLDSGVERAIIGTAALRQPEILEQACGLYRS 122 VV ++ K + IP VGGGI +++ +R L +G E+ + + A++ P+I+ Q + + Sbjct: 63 LDVVEAVAKQIFIPFSVGGGINSVDDMRAVLRAGAEKVSVNSGAVKNPDIISQGAAQFGA 122 Query: 123 R-IALGIDAR---------DGL-VAIEGWKETSGTDAVALAKRFEKLDLAAIIYTDIHRD 171 + + LG+D + G + I G ++ G DA+ AK E L I I D Sbjct: 123 QCVVLGMDVKRVPVTKDIPSGFEIVIHGGRKHMGMDAIEWAKTGEALGAGEICLNSIDAD 182 Query: 172 GMQSGVNIEATKRLLESCSIPVIASGGV----HTLQDIED 207 G + G +IE T++++++ SIPVIASGG H ++ + D Sbjct: 183 GTKDGYDIELTRKVVQAVSIPVIASGGAGHPEHMVEAVTD 222 Score = 33.9 bits (76), Expect = 3e-06 Identities = 21/74 (28%), Positives = 37/74 (50%) Query: 29 GKDPVSVAKRWEGEGAGWLHVVDLDGAFLRRPANRQVVASIVKAVSIPVQVGGGIRNLEA 88 G D + AK E GAG + + +D + + ++ +V+AVSIPV GG + E Sbjct: 156 GMDAIEWAKTGEALGAGEICLNSIDADGTKDGYDIELTRKVVQAVSIPVIASGGAGHPEH 215 Query: 89 IRDYLDSGVERAII 102 + + + G+ A + Sbjct: 216 MVEAVTDGMASAAL 229 Lambda K H 0.321 0.140 0.413 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: 190 Number of extensions: 10 Number of successful extensions: 3 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: 256 Length of database: 259 Length adjustment: 24 Effective length of query: 232 Effective length of database: 235 Effective search space: 54520 Effective search space used: 54520 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 (21.8 bits) S2: 47 (22.7 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