Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate WP_012676575.1 PERMA_RS08165 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase
Query= BRENDA::Q8ZY16 (253 letters) >NCBI__GCF_000021565.1:WP_012676575.1 Length = 241 Score = 113 bits (283), Expect = 3e-30 Identities = 78/240 (32%), Positives = 130/240 (54%), Gaps = 11/240 (4%) Query: 7 IIPCLDI-DGKAGVVVKGVNFQGIREVGD-PVEMAVRYEEEGADEIAILDITAAPEGRAT 64 +IP +DI DGKA + KG + + + GD PV +A ++EE+GA + I+D+ A EG+ Sbjct: 7 VIPAVDIKDGKAVRLYKG-DPEAVTVYGDDPVSVAKQWEEKGAKHLHIVDLDGAFEGKPK 65 Query: 65 FIDSVKRVAEAVSIPVLVGGGVRSLEDATTLFRAGADKVSVNTAAVRNPQLVALLAREFG 124 ID VK + + VSIPV GGG+RS E ++ G ++V + + A +N Q + + Sbjct: 66 NIDIVKDIVKTVSIPVEFGGGLRSFEAVKSIVETGVERVVIGSLAYQNRQEFERIVSAYP 125 Query: 125 SQSTVVAIDAKWNGEYYEVYVKGGREATGLDAVKWAKEVEELGAGEILLTSIDRDGTGLG 184 + +V IDAK +V +KG E T + +A+ ++L L T ++RDG +G Sbjct: 126 GK-VIVGIDAKDG----KVAIKGWLEKTEYTPLDFARMFDDLDIWGFLYTDVNRDGAMVG 180 Query: 185 YDVELIRRVADSVRIPVIASGGAGRVE---HFYEAAAAGADAVLAASLFHFRVLSIAQVK 241 ++E + +A +++ PVIASGG G VE Y+ G V+ + + + Q++ Sbjct: 181 PNIEGTKYLAQNLKHPVIASGGVGSVEDLKKLYDLKKYGVYGVVVGKALYEGKIKLEQLE 240 Lambda K H 0.318 0.137 0.381 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: 169 Number of extensions: 13 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: 253 Length of database: 241 Length adjustment: 24 Effective length of query: 229 Effective length of database: 217 Effective search space: 49693 Effective search space used: 49693 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