Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate WP_012505033.1 PAES_RS02210 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= BRENDA::Q8ZY16 (253 letters) >NCBI__GCF_000020625.1:WP_012505033.1 Length = 261 Score = 109 bits (273), Expect = 5e-29 Identities = 71/201 (35%), Positives = 106/201 (52%), Gaps = 5/201 (2%) Query: 7 IIPCLDI-DGKAGVVVKGVNFQGIREVGDPVEMAVRYEEEGADEIAILDITAAPEGRATF 65 IIP +DI DGK + +G Q + +P +MA+ + ++ A + ++D+ AA G Sbjct: 3 IIPAIDIKDGKCVRLTRGDFDQQKIYLDNPRDMAIIWRKQNAKMLHVVDLDAALTGTMVN 62 Query: 66 IDSVKRVAEAVSIPVLVGGGVRSLEDATTLFRAGADKVSVNTAAVRNPQLVALLAREFGS 125 + ++ + + IPV VGGG+RS ED G +V + +AAV NPQL+A L F Sbjct: 63 FEKIREIVATLDIPVQVGGGIRSFEDVERYLGIGVSRVVIGSAAVTNPQLIAELLATFSP 122 Query: 126 QSTVVAIDAKWNGEYYEVYVKGGREATGLDAVKWAKEVEELGAGEILLTSIDRDGTGLGY 185 VV IDA+ NG +KG E++ + + A E+++LG I+ T I RDG G Sbjct: 123 SQIVVGIDAE-NG---IPKIKGWTESSSMQDYELALEMKKLGVKRIIYTDISRDGMMQGV 178 Query: 186 DVELIRRVADSVRIPVIASGG 206 E RR A + V ASGG Sbjct: 179 GYESTRRFAMKAGMRVTASGG 199 Score = 29.3 bits (64), Expect = 8e-05 Identities = 22/75 (29%), Positives = 33/75 (44%), Gaps = 3/75 (4%) Query: 37 EMAVRYEEEGADEIAILDITAAPEGRATFIDSVKRVAEAVSIPVLVGGGVRSLED---AT 93 E+A+ ++ G I DI+ + +S +R A + V GGV S +D Sbjct: 151 ELALEMKKLGVKRIIYTDISRDGMMQGVGYESTRRFAMKAGMRVTASGGVTSSDDLKKLQ 210 Query: 94 TLFRAGADKVSVNTA 108 TL + G D V V A Sbjct: 211 TLEQYGVDSVIVGKA 225 Score = 25.8 bits (55), Expect = 0.001 Identities = 19/73 (26%), Positives = 29/73 (39%), Gaps = 4/73 (5%) Query: 156 AVKWAKEVEELGAGEILLTSIDRDGTGLGYDVELIRRVADSVRIPVIASGGAGRVEHFYE 215 A+ W K+ A + + +D TG + E IR + ++ IPV GG E Sbjct: 36 AIIWRKQ----NAKMLHVVDLDAALTGTMVNFEKIREIVATLDIPVQVGGGIRSFEDVER 91 Query: 216 AAAAGADAVLAAS 228 G V+ S Sbjct: 92 YLGIGVSRVVIGS 104 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: 189 Number of extensions: 13 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 253 Length of database: 261 Length adjustment: 24 Effective length of query: 229 Effective length of database: 237 Effective search space: 54273 Effective search space used: 54273 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: 47 (22.7 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