Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate WP_014026985.1 PYRFU_RS07130 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
Query= BRENDA::Q8ZY16 (253 letters) >NCBI__GCF_000223395.1:WP_014026985.1 Length = 235 Score = 92.0 bits (227), Expect = 9e-24 Identities = 72/237 (30%), Positives = 117/237 (49%), Gaps = 15/237 (6%) Query: 8 IPCLDIDGKAGVVVK---GVNFQGIREVGDPVEMAVRYEEEGADEIAILDITAAPEGRAT 64 +P LD++ AG VVK GV G+ VG P+E+A R E+G + + ++D+ A G+ Sbjct: 1 MPSLDLE--AGRVVKRVEGVKGTGL-VVGSPLEVAKRLWEKGVEWLHVVDLDGAEAGKPV 57 Query: 65 FIDSVKRVAEAVSIPVLVGGGVRSLEDATTLF-RAGADKVSVNTAAVRNPQLVALLAREF 123 + + + + V GGG+R+ E L + G ++V + T RNP+LV + E+ Sbjct: 58 NVGIAESLVR-MGFHVQYGGGIRAKEHVELLLDKIGVERVVIGTLVHRNPRLVEDVVEEY 116 Query: 124 GSQSTVVAIDAKWNGEYYEVYVKGGR-EATGLDAVKWAKEVEELGAGEILLTSIDRDGTG 182 G V A+DAKW V ++G R EA L + V LG +IL TS++R+G Sbjct: 117 GGDRIVAALDAKWG----MVVIEGWRKEAKSLRDM--LDLVYGLGVRQILYTSVEREGKL 170 Query: 183 LGYDVELIRRVADSVRIPVIASGGAGRVEHFYEAAAAGADAVLAASLFHFRVLSIAQ 239 G D+E + + + +GG ++ A G DA + FH +L + + Sbjct: 171 TGADLERVAWLRGVWPYGLQYAGGIATIDDILGLAELGVDAAILGMAFHAGLLDVVE 227 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: 181 Number of extensions: 20 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: 235 Length adjustment: 24 Effective length of query: 229 Effective length of database: 211 Effective search space: 48319 Effective search space used: 48319 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