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 3609190 Dshi_2576 imidazoleglycerol phosphate synthase, cyclase subunit (RefSeq)
Query= curated2:Q0W0J3 (240 letters) >FitnessBrowser__Dino:3609190 Length = 253 Score = 127 bits (320), Expect = 2e-34 Identities = 80/245 (32%), Positives = 136/245 (55%), Gaps = 17/245 (6%) Query: 1 MSFNVIPAIDLKGGKCVQLVQGVPGTEMVSIDDAVEVAAGWVGQGAKTLHIIDLDGAFSG 60 + VIP +D+ G+ +V+GV ++V D VE A + GA L +D+ Sbjct: 2 LKIRVIPCLDVADGR---VVKGVNFVDLVDAGDPVESAKAYDAAGADELCFLDIHA---- 54 Query: 61 SRKNAYIMEDIVSKFD----VDVQVGGGIRDYETAKYLLSLGIDRVILGTAAIKNPDLVR 116 + +N M D+ ++ + + +GGG+R E + LL G D+V +AA+ +PD++ Sbjct: 55 TNENRGTMYDLATRTAEQCFMPLTIGGGVRTTEDVRNLLLAGADKVSFNSAAVADPDVIA 114 Query: 117 QLADEFGSETVMVSLDSK-----QGEVVIEGWTESSGKTTNEMGKFFSEIGAGSILYTNV 171 + AD+FGS+ ++ ++D+K + E+ G + +G E K E GAG IL T++ Sbjct: 115 RAADKFGSQCIVCAIDAKTVAPGRWEIFTHGGRKPTGIDAVEFAKTVVEKGAGEILLTSM 174 Query: 172 DVEGLLKGVNEDPVRSLVNSVTIPVIASGGVAKIDDLVK-IKNTGAAGVVVGSALYKGLF 230 D +G +G N R++ ++V++PVIASGGV +D LV+ + GA+ V+ S + G F Sbjct: 175 DRDGTKQGFNIALTRAISDAVSVPVIASGGVGTLDHLVEGVTEGGASAVLAASIFHFGEF 234 Query: 231 TLREA 235 T+REA Sbjct: 235 TIREA 239 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: 171 Number of extensions: 11 Number of successful extensions: 4 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: 253 Length adjustment: 24 Effective length of query: 216 Effective length of database: 229 Effective search space: 49464 Effective search space used: 49464 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 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