Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate HSERO_RS20320 HSERO_RS20320 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
Query= BRENDA::A4WHB6 (251 letters) >FitnessBrowser__HerbieS:HSERO_RS20320 Length = 265 Score = 96.3 bits (238), Expect = 6e-25 Identities = 70/233 (30%), Positives = 116/233 (49%), Gaps = 19/233 (8%) Query: 5 VIPCLDM-DGKAGVVVKGVNFEGVREVGDPVEMAVRYEEEGADEIAILDITATPEGRSTF 63 +IP +D+ DG + +G + DP EMA+ + ++GA + ++D+ G+ Sbjct: 3 LIPAIDLKDGHCVRLKQGDMDQATVFSEDPAEMALHWLKQGARRLHLVDLNGAFAGKPKN 62 Query: 64 VESVRRVAEAVS----------IPVLVGGGVRGIEDAAALFKAGADKVSVNTAAVKNPRL 113 +V+ + +AV+ IPV +GGG+R ++ G + + TAAVKNP Sbjct: 63 EAAVKAILKAVASFAEENEVEEIPVQLGGGIRDLDTIERYLDDGLSYIIIGTAAVKNPGF 122 Query: 114 VSEIAREFGSQSTVVAIDAKLVGGRYEVFVRGGKEPTGLDAVEWAKKVEELGAGEILLTS 173 + + F Q +V +DAK +V G + +G + V+ A+K E G I+ T Sbjct: 123 LHDACSAFPGQ-IIVGLDAK----DGKVATDGWSKLSGHEVVDLAQKFEGYGCEAIVYTD 177 Query: 174 IDKDGTRLGYDVELIRRVAEAVKIPVIASGG---AGALEHFYEAAAAGADAVL 223 I +DG G ++E R+A+AV IP+IASGG G +E G +AV+ Sbjct: 178 IGRDGMMGGVNIEATVRLAQAVTIPIIASGGVHNVGDVEALCRVEDEGIEAVI 230 Lambda K H 0.318 0.136 0.375 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: 165 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: 251 Length of database: 265 Length adjustment: 24 Effective length of query: 227 Effective length of database: 241 Effective search space: 54707 Effective search space used: 54707 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: 41 (21.7 bits) S2: 47 (22.7 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