Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate WP_028487400.1 B076_RS0111215 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= BRENDA::A4WHB6 (251 letters) >NCBI__GCF_000483485.1:WP_028487400.1 Length = 247 Score = 107 bits (268), Expect = 2e-28 Identities = 71/223 (31%), Positives = 115/223 (51%), Gaps = 7/223 (3%) Query: 5 VIPCLDM-DGKAGVVVKGVNFEGVREVGDPVEMAVRYEEEGADEIAILDITATPEGRSTF 63 +IP +D+ DG+ + +G+ + GD V MA R+ ++GA + ++D+ EG+ Sbjct: 3 LIPAIDLKDGQCVRLRQGIMEDATVFSGDIVAMAERWVDQGARRLHMVDLNGAFEGKPVN 62 Query: 64 VESVRRVAEAV-SIPVLVGGGVRGIEDAAALFKAGADKVSVNTAAVKNPRLVSEIAREFG 122 E+V +V EA +P+ +GGG+R ++ A AG + T AV NP V+E + F Sbjct: 63 GEAVYQVREAYPDLPIQIGGGIRDLQTIEAYLNAGVSYCIIGTKAVHNPEFVAEACQAFP 122 Query: 123 SQSTVVAIDAKLVGGRYEVFVRGGKEPTGLDAVEWAKKVEELGAGEILLTSIDKDGTRLG 182 +V +DAK V + G E T + + K+ E G I+ T I +DG G Sbjct: 123 GH-IMVGLDAK----EGMVAINGWAEVTDHEVTQLGKQFENDGVEAIIYTDIGRDGMMQG 177 Query: 183 YDVELIRRVAEAVKIPVIASGGAGALEHFYEAAAAGADAVLAA 225 ++E + +A+A+ IP+IASGG L+ A+ AD V A Sbjct: 178 VNIEATQALAKALNIPIIASGGITNLDDIRRLASIEADGVSGA 220 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: 150 Number of extensions: 15 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: 247 Length adjustment: 24 Effective length of query: 227 Effective length of database: 223 Effective search space: 50621 Effective search space used: 50621 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: 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