Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate WP_011033450.1 MM_RS07770 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase
Query= BRENDA::A4WHB6 (251 letters) >NCBI__GCF_000007065.1:WP_011033450.1 Length = 246 Score = 141 bits (355), Expect = 1e-38 Identities = 82/241 (34%), Positives = 128/241 (53%), Gaps = 8/241 (3%) Query: 1 MAVRVIPCLDM-DGKAGVVVKGVNFEGVREVGDPVEMAVRYEEEGADEIAILDITATPEG 59 M VIP +DM GK +V+GV + + DP+ +A+ + +GA + ++D+ EG Sbjct: 1 MVFEVIPAVDMRGGKCVQLVQGVPGSEIVSIDDPLAVALDWVSKGAKTLHLVDLDGAIEG 60 Query: 60 R---STFVESVRRVAEAVSIPVLVGGGVRGIEDAAALFKAGADKVSVNTAAVKNPRLVSE 116 S +E + + + + VGGG+R EDAA+L + G ++ + TAA++NP LV + Sbjct: 61 ERKNSPIIEKIVNTCKEKGVSIQVGGGIRSFEDAASLLEIGVSRIILGTAALQNPELVKQ 120 Query: 117 IAREFGSQSTVVAIDAKLVGGRYEVFVRGGKEPTGLDAVEWAKKVEELGAGEILLTSIDK 176 ++ FGS VA+DAK ++ ++G E VE +K EELGAG +L T+ID Sbjct: 121 LSSSFGSSHVNVALDAK----NGKISIKGWTEECAQTPVEMGRKFEELGAGSLLFTNIDT 176 Query: 177 DGTRLGYDVELIRRVAEAVKIPVIASGGAGALEHFYEAAAAGADAVLAASLFHFRVLTIS 236 +G G + + + E+V IPVIASGG LE GA V+ S + T+ Sbjct: 177 EGLMQGVNPVPTKELVESVSIPVIASGGVSTLEDIKTLKKTGAAGVVVGSALYMGRFTLE 236 Query: 237 E 237 E Sbjct: 237 E 237 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: 174 Number of extensions: 15 Number of successful extensions: 5 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: 246 Length adjustment: 24 Effective length of query: 227 Effective length of database: 222 Effective search space: 50394 Effective search space used: 50394 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