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_011649867.1 RL_RS00210 imidazole glycerol phosphate synthase subunit HisF
Query= curated2:Q0W0J3 (240 letters) >NCBI__GCF_000009265.1:WP_011649867.1 Length = 262 Score = 120 bits (302), Expect = 2e-32 Identities = 80/249 (32%), Positives = 131/249 (52%), Gaps = 25/249 (10%) Query: 5 VIPAIDLKGGKCVQLVQGVPGTEMVSIDDAVEVAAGWVGQGAKTLHIIDLDGAFSGSRKN 64 VIP +D+K G+ +V+GV +V D VE A + GA L +D+ + S N Sbjct: 7 VIPCLDVKDGR---VVKGVNFLNLVDAGDPVEAAKAYDAAGADELCFLDI----TASSDN 59 Query: 65 AYIMEDIVSKFD----VDVQVGGGIRDYETAKYLLSLGIDRVILGTAAIKNPDLVRQLAD 120 + D+VS+ + + VGGG+R + LL G D+V + +AA+ NPD V + AD Sbjct: 60 RETIFDVVSRTADQCFMPLTVGGGVRTIADIRKLLLCGADKVSINSAAVSNPDFVTEAAD 119 Query: 121 EFGSETVMVSLDSKQ-------------GEVVIEGWTESSGKTTNEMGKFFSEIGAGSIL 167 +FG + ++VS+D+K+ E+ G ++G E + GAG +L Sbjct: 120 KFGDQCIVVSIDAKRRRTQAVGGDNLSAWEIYTHGGRNATGIDAVEFAQKMVARGAGELL 179 Query: 168 YTNVDVEGLLKGVNEDPVRSLVNSVTIPVIASGGVAKIDDLVK-IKNTGAAGVVVGSALY 226 T++D +G G + + R++ ++V +PVIASGGV +DDLV +K A V+ S + Sbjct: 180 VTSMDRDGTKVGYDLELTRAIADAVRVPVIASGGVGDLDDLVAGVKEGHANAVLAASIFH 239 Query: 227 KGLFTLREA 235 G +++ EA Sbjct: 240 FGTYSVSEA 248 Lambda K H 0.315 0.136 0.378 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: 152 Number of extensions: 10 Number of successful extensions: 2 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: 240 Length of database: 262 Length adjustment: 24 Effective length of query: 216 Effective length of database: 238 Effective search space: 51408 Effective search space used: 51408 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: 42 (22.0 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