Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate WP_011868972.1 MMARC5_RS06185 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase
Query= BRENDA::A4WHB6 (251 letters) >NCBI__GCF_000016125.1:WP_011868972.1 Length = 238 Score = 139 bits (351), Expect = 4e-38 Identities = 75/234 (32%), Positives = 133/234 (56%), Gaps = 5/234 (2%) Query: 5 VIPCLDMDGKAGV-VVKGVNFEGVREVGDPVEMAVRYEEEGADEIAILDITATPEGRSTF 63 VIP +DM K V +++G + E+ +P E+A ++ EGA+ + ++D+ +G+ Sbjct: 3 VIPAVDMKNKKCVQLIQGNPDKKHVELDNPPEIAKKWVSEGAEMLHLVDLDGALDGKRVN 62 Query: 64 VESVRRVAEAVSIPVLVGGGVRGIEDAAALFKAGADKVSVNTAAVKNPRLVSEIAREFGS 123 E + + + +PV +GGG+R IEDA L + GA KV + T AV+ P ++ E++ GS Sbjct: 63 DEFIEEIIKTSGVPVQIGGGIRSIEDAVYLVEKGAKKVIIGTIAVEKPEIIKELSENIGS 122 Query: 124 QSTVVAIDAKLVGGRYEVFVRGGKEPTGLDAVEWAKKVEELGAGEILLTSIDKDGTRLGY 183 + +V++DAK +V ++G KE T VE K +EE+GAG IL T++D +G G Sbjct: 123 EKIMVSLDAK----DGKVVIKGWKEKTKYTPVEIGKILEEMGAGSILFTNVDSEGLLNGI 178 Query: 184 DVELIRRVAEAVKIPVIASGGAGALEHFYEAAAAGADAVLAASLFHFRVLTISE 237 ++E + + E +KIP++ASGG ++ + G V+ S + ++ + + Sbjct: 179 NIEPTKELVENLKIPIVASGGVTTIDDLLKFKEIGVYGVVVGSAIYKNMINLKD 232 Score = 26.2 bits (56), Expect = 6e-04 Identities = 25/98 (25%), Positives = 41/98 (41%), Gaps = 4/98 (4%) Query: 156 EWAKKVEELGAGEILLTSIDK--DGTRLGYDVELIRRVAEAVKIPVIASGGAGALEHFYE 213 E AKK GA + L +D DG R+ + E I + + +PV GG ++E Sbjct: 34 EIAKKWVSEGAEMLHLVDLDGALDGKRV--NDEFIEEIIKTSGVPVQIGGGIRSIEDAVY 91 Query: 214 AAAAGADAVLAASLFHFRVLTISEVKRYLRQRGVEVRL 251 GA V+ ++ + I E+ + + V L Sbjct: 92 LVEKGAKKVIIGTIAVEKPEIIKELSENIGSEKIMVSL 129 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: 155 Number of extensions: 12 Number of successful extensions: 4 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: 238 Length adjustment: 24 Effective length of query: 227 Effective length of database: 214 Effective search space: 48578 Effective search space used: 48578 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