Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate WP_086508672.1 BZY95_RS03885 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= BRENDA::A4WHB6 (251 letters) >NCBI__GCF_002151265.1:WP_086508672.1 Length = 250 Score = 106 bits (264), Expect = 5e-28 Identities = 75/225 (33%), Positives = 110/225 (48%), Gaps = 11/225 (4%) Query: 5 VIPCLDM-DGKAGVVVKGVNFEGVREVGDPVEMAVRYEEEGADEIAILDITATPEGRSTF 63 VIP +D+ DGK + +G + DPV MA R+ E GA + ++D+ EG+ Sbjct: 3 VIPAIDLKDGKCVRLKQGRMDDATTYGDDPVAMAARWVEAGARRLHLVDLNGAFEGKPIN 62 Query: 64 VESVRRVAEA-VSIPVLVGGGVRGIEDAAALFKAGADKVSVNTAAVKNPRLVSEIAREFG 122 E+V +A +P+ +GGG+R E AG V + T AVK P V E+ R F Sbjct: 63 GEAVTAIARRWPELPIQIGGGIRSAETIEHYLAAGVSYVIIGTKAVKEPAFVGEVCRAFP 122 Query: 123 SQSTVVAIDAKLVGGRYEVFVR--GGKEPTGLDAVEWAKKVEELGAGEILLTSIDKDGTR 180 +V +DA+ + FV G E + + AV+ AK+ + G I+ T I +DG Sbjct: 123 GH-VIVGLDAR------DGFVATDGWAEVSQVKAVDLAKRFADDGVSSIVYTDIARDGMM 175 Query: 181 LGYDVELIRRVAEAVKIPVIASGGAGALEHFYEAAAAGADAVLAA 225 G +VE +A +PVIASGG L+ AAG +L A Sbjct: 176 NGVNVEATAELAREGGLPVIASGGVTNLDDLRALVAAGEPGILGA 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: 156 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: 251 Length of database: 250 Length adjustment: 24 Effective length of query: 227 Effective length of database: 226 Effective search space: 51302 Effective search space used: 51302 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