Align imidazole glycerol-phosphate synthase (EC 4.3.2.10) (characterized)
to candidate WP_013643735.1 METBO_RS00655 imidazole glycerol phosphate synthase subunit HisF
Query= BRENDA::Q9SZ30 (592 letters) >NCBI__GCF_000191585.1:WP_013643735.1 Length = 274 Score = 200 bits (508), Expect = 7e-56 Identities = 126/312 (40%), Positives = 174/312 (55%), Gaps = 40/312 (12%) Query: 280 LAKRVIACLDVRTNDKGDLVVTKGDQYDVREQSNENEVRNLGKPVDLAGQYYKDGADEIS 339 LAKR+I CLD N VV KG ++ E+R G PV+LA +YY+DGADEI Sbjct: 2 LAKRIIPCLDCDLNVPHGRVV-KGVEF--------KEIRYAGDPVELATRYYEDGADEIV 52 Query: 340 FLNITGFRDFPLGDLPMIQVLRQTSKNVFVPLTVGGGIRDFTDASGRYYSSLEVAAEYFR 399 FL+IT + M V++ T++NVFVP+ VGGGIR D Y + L R Sbjct: 53 FLDITASHE---RRETMADVIKATTENVFVPICVGGGIRKPDD----YVNML-------R 98 Query: 400 SGADKISIGSDAVSAAEEFIKSGVKTGKSSLEQISRVYGNQAVVVSIDPRRVYVNHPDDV 459 +GADK S + A+ + + + S++ G+QA V+ ID +R YV+ P + Sbjct: 99 AGADKCSTNTAAIHNPD------------LINEASKIVGSQACVIGIDAKRRYVSDPSEK 146 Query: 460 PYKVIRVTNPGPNGEEYAWYQCTVSGGREGRPIGAFELAKAVEELGAGEILLNCIDCDGQ 519 P K++ T G Y W+ C++ GGRE I A A +E GAGEILL +D DG Sbjct: 147 PEKIVVETKKG-----YCWFDCSIYGGREFTGIDALAWAIECQERGAGEILLTSMDRDGT 201 Query: 520 GKGFDIDLVKLISDSVGIPVIASSGAGTPDHFSEVFEKTNASAALAAGIFHRKEVPIQSV 579 G+D++L + +S+++ IPVIAS G G P H E FE A AALAA IFH E P+ V Sbjct: 202 KDGYDLELTRTMSENLDIPVIASGGVGNPQHIYEAFEIGKADAALAASIFHFNEYPVPEV 261 Query: 580 KEHLQEERIEVR 591 K++L ++ I VR Sbjct: 262 KKYLVDKGIPVR 273 Lambda K H 0.317 0.135 0.391 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: 396 Number of extensions: 24 Number of successful extensions: 7 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: 592 Length of database: 274 Length adjustment: 31 Effective length of query: 561 Effective length of database: 243 Effective search space: 136323 Effective search space used: 136323 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 (21.6 bits) S2: 50 (23.9 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