Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate WP_011386876.1 AMB_RS22930 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase
Query= BRENDA::A4WHB6 (251 letters) >NCBI__GCF_000009985.1:WP_011386876.1 Length = 239 Score = 103 bits (257), Expect = 3e-27 Identities = 70/205 (34%), Positives = 107/205 (52%), Gaps = 6/205 (2%) Query: 5 VIPCLDMDGKAGVVVK-GVNFEGVREVGDPVEMAVRYEEEGADEIAILDITATPEGRSTF 63 + P +D+ A V +K G+ E DP A + GA+ I ++D+ G+ Sbjct: 3 LFPAIDLKDGACVRLKLGLMEESTVFNTDPGAQARDFAAAGAEWIHVVDLNGAFAGKPVN 62 Query: 64 VESVRRVAEAVSIPVLVGGGVRGIEDAAALFKAGADKVSVNTAAVKNPRLVSEIAREFGS 123 +V + ++VS+PV +GGG+R + G +V + T A+KNP LV E + F Sbjct: 63 GAAVDSILKSVSVPVQLGGGIREMATIEDWLARGIRRVILGTVALKNPALVKEACQRFPG 122 Query: 124 QSTVVAIDAKLVGGRYEVFVRGGKEPTGLDAVEWAKKVEELGAGEILLTSIDKDGTRLGY 183 + V IDAK GG+ V V G E + L +E A+K E+ G ++ T ID+DG G Sbjct: 123 R-VAVGIDAK--GGK--VAVEGWAETSDLTVLELARKFEDCGVAALIYTDIDRDGVLAGP 177 Query: 184 DVELIRRVAEAVKIPVIASGGAGAL 208 +V +A+A+ IPVIASGG +L Sbjct: 178 NVAATAALADAISIPVIASGGVSSL 202 Score = 37.4 bits (85), Expect = 3e-07 Identities = 27/82 (32%), Positives = 40/82 (48%), Gaps = 4/82 (4%) Query: 16 GVVVKG--VNFEGVREVGD--PVEMAVRYEEEGADEIAILDITATPEGRSTFVESVRRVA 71 G+ KG V EG E D +E+A ++E+ G + DI V + +A Sbjct: 127 GIDAKGGKVAVEGWAETSDLTVLELARKFEDCGVAALIYTDIDRDGVLAGPNVAATAALA 186 Query: 72 EAVSIPVLVGGGVRGIEDAAAL 93 +A+SIPV+ GGV + D AL Sbjct: 187 DAISIPVIASGGVSSLVDLKAL 208 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: 163 Number of extensions: 13 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 251 Length of database: 239 Length adjustment: 24 Effective length of query: 227 Effective length of database: 215 Effective search space: 48805 Effective search space used: 48805 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 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