Align imidazole glycerol-phosphate synthase (EC 4.3.2.10) (characterized)
to candidate WP_028950472.1 Q385_RS0104230 imidazole glycerol phosphate synthase subunit HisF
Query= BRENDA::Q9SZ30 (592 letters) >NCBI__GCF_000619805.1:WP_028950472.1 Length = 252 Score = 181 bits (460), Expect = 2e-50 Identities = 124/316 (39%), Positives = 177/316 (56%), Gaps = 68/316 (21%) Query: 280 LAKRVIACLDVRTNDKGDLVVTKGDQYDVREQSNENEVRNLGKPVDLAGQYYKDGADEIS 339 LAKR+I CLDV +KG +V KG N + + G PV++A Y K+GADEI Sbjct: 2 LAKRIIPCLDV---NKGRVV--KG--------VNFVNLIDAGDPVEIAAAYDKEGADEIV 48 Query: 340 FLNITGF---RDFPLGDLPMIQVLRQTSKNVFVPLTVGGGIRDFTDASGRYYSSLEVAAE 396 FL+IT RD ++ V+++T++ VF+PLTVGGG+R SLE + Sbjct: 49 FLDITASAEDRDI------ILDVVKKTAETVFMPLTVGGGVR-----------SLEDIRK 91 Query: 397 YFRSGADKISIGSDAVSAAEEFIKSGVKTGKSSLEQISRVYGNQAVVVSIDPRRVYVNHP 456 +GADK+SI + AV S +E + +G+ +VV+ID +++ Sbjct: 92 LLENGADKVSINTAAVK------------NPSLVESAAVRFGSSTIVVAIDAKKI----- 134 Query: 457 DDVPYKVIRVTNPGPNGEEYAWYQCTVSGGREGRPIGAFELAKAVEELGAGEILLNCIDC 516 +E W + ++GGR I A + AKAVE+LGAGEILL +D Sbjct: 135 -----------------DENKW-EVYINGGRTPTGIDAVQWAKAVEDLGAGEILLTSMDK 176 Query: 517 DGQGKGFDIDLVKLISDSVGIPVIASSGAGTPDHFSEVFEKTNASAALAAGIFHRKEVPI 576 DG G+D++L K +S++V IPVIAS GAG +HF EVFE+ A AALAA +FH KEV I Sbjct: 177 DGTKSGYDVELTKAVSEAVKIPVIASGGAGKKEHFYEVFEEGKADAALAASLFHFKEVGI 236 Query: 577 QSVKEHLQEERIEVRI 592 + +K+ L+E+ + VRI Sbjct: 237 KELKQFLKEKNVNVRI 252 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: 362 Number of extensions: 28 Number of successful extensions: 8 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: 252 Length adjustment: 30 Effective length of query: 562 Effective length of database: 222 Effective search space: 124764 Effective search space used: 124764 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 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