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 AZOBR_RS01685 AZOBR_RS01685 imidazole glycerol phosphate synthase
Query= curated2:A0B7W4 (242 letters) >FitnessBrowser__azobra:AZOBR_RS01685 Length = 265 Score = 129 bits (323), Expect = 8e-35 Identities = 81/237 (34%), Positives = 135/237 (56%), Gaps = 9/237 (3%) Query: 5 IFPAVDLRGGRCVQLVQGVPGSEVVSLDDPLVQAVRWADMGADHLHIIDLDGAIEGTRLN 64 + P +D++ GR +V+GV +++ DP+ QA + GAD L +D+ + E Sbjct: 6 VIPCLDVKDGR---VVKGVNFVDLIDAGDPVEQARVYDREGADELTFLDITASHENRDTI 62 Query: 65 APILRRIVGELEVFVQVGGGIRSRSDVAEVLDTGVDRVILGTMALRDPPVVKELAEEYGP 124 ++RR ++ + + VGGG+R+ D+ ++L G D+V + T A+ P V+E AE++G Sbjct: 63 YDVVRRTAEQVFMPLTVGGGVRTVEDIRKLLLAGADKVSINTAAIHRPEFVQEAAEKFGA 122 Query: 125 DRIMVALD---VRDGR--VTSEGWQRTLEFDAIELGIVFESFGAGSILFTNIDTEGQQRG 179 I+VA+D V GR + + G ++ DAIE ES+GAG IL T++D +G + G Sbjct: 123 QCIVVAIDAKQVEPGRWEIFTHGGRKATGIDAIEWAKRMESYGAGEILLTSMDRDGTKSG 182 Query: 180 VDPEPTRELVEAVSIPVIAAGGVSSLDDIKLLSDAGAAGAVIGTAIY-TGTLNLREA 235 D TR++ + + IPVIA+GGV +LD + G A AV+ +I+ GT + +A Sbjct: 183 FDLALTRKVADGLRIPVIASGGVGTLDHLVEGIREGHATAVLAASIFHFGTYTIGQA 239 Score = 48.9 bits (115), Expect = 1e-10 Identities = 36/119 (30%), Positives = 56/119 (47%), Gaps = 12/119 (10%) Query: 126 RIMVALDVRDGRVTSEGWQRTLEF-------DAIELGIVFESFGAGSILFTNIDTEGQQR 178 R++ LDV+DGRV + + F D +E V++ GA + F +I + R Sbjct: 5 RVIPCLDVKDGRVV-----KGVNFVDLIDAGDPVEQARVYDREGADELTFLDITASHENR 59 Query: 179 GVDPEPTRELVEAVSIPVIAAGGVSSLDDIKLLSDAGAAGAVIGTAIYTGTLNLREALE 237 + R E V +P+ GGV +++DI+ L AGA I TA ++EA E Sbjct: 60 DTIYDVVRRTAEQVFMPLTVGGGVRTVEDIRKLLLAGADKVSINTAAIHRPEFVQEAAE 118 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: 181 Number of extensions: 10 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: 242 Length of database: 265 Length adjustment: 24 Effective length of query: 218 Effective length of database: 241 Effective search space: 52538 Effective search space used: 52538 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 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