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_011800115.1 PNAP_RS03470 imidazole glycerol phosphate synthase cyclase subunit
Query= curated2:A0B7W4 (242 letters) >NCBI__GCF_000015505.1:WP_011800115.1 Length = 259 Score = 130 bits (328), Expect = 2e-35 Identities = 77/234 (32%), Positives = 126/234 (53%), Gaps = 15/234 (6%) Query: 5 IFPAVDLRGGRCVQLVQGVPGSEVVSLDDPLVQAVRWADMGADHLHIIDLDGAIEGTRLN 64 I P +D+ GGR +V+GV E+ DP+ A R+ D GAD L +D+ +G L Sbjct: 6 IIPCLDVTGGR---VVKGVNFVELRDAGDPVEIAARYNDQGADELTFLDITATSDGRDLI 62 Query: 65 APILRRIVGELEVFVQVGGGIRSRSDVAEVLDTGVDRVILGTMALRDPPVVKELAEEYGP 124 I+ + ++ + + VGGG+R+ DV +L+ G D+ + AL +P V+ + + +YG Sbjct: 63 LHIIEAVASQVFIPLTVGGGVRTVEDVRRLLNAGADKTSFNSAALANPQVITDASAKYGA 122 Query: 125 DRIMVALDVR-----DGRVTSEGW-------QRTLEFDAIELGIVFESFGAGSILFTNID 172 I+VA+D + D + GW ++ DA+ + GAG IL T+++ Sbjct: 123 QCIVVAIDAKRRSDEDALLRGAGWDVYSHGGRKNTGLDAVAWAVEMAQRGAGEILLTSMN 182 Query: 173 TEGQQRGVDPEPTRELVEAVSIPVIAAGGVSSLDDIKLLSDAGAAGAVIGTAIY 226 +G + G D E TR + +AVS+PVIA+GGV +LD + G A AV+ +I+ Sbjct: 183 RDGTKSGFDLELTRAVSDAVSVPVIASGGVGNLDHLADGVQLGGADAVLAASIF 236 Lambda K H 0.319 0.140 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: 192 Number of extensions: 13 Number of successful extensions: 3 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: 242 Length of database: 259 Length adjustment: 24 Effective length of query: 218 Effective length of database: 235 Effective search space: 51230 Effective search space used: 51230 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: 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