Align imidazole glycerol-phosphate synthase (EC 4.3.2.10) (characterized)
to candidate WP_012284027.1 HM1_RS13855 imidazole glycerol phosphate synthase cyclase subunit
Query= BRENDA::Q9SZ30 (592 letters) >NCBI__GCF_000019165.1:WP_012284027.1 Length = 261 Score = 173 bits (438), Expect = 9e-48 Identities = 119/312 (38%), Positives = 158/312 (50%), Gaps = 56/312 (17%) Query: 280 LAKRVIACLDVRTNDKGDLVVTKGDQYDVREQSNENEVRNLGKPVDLAGQYYKDGADEIS 339 LAKR+I CLDV V KG +N +R+ G PV+LA Y K+GADE+ Sbjct: 2 LAKRIIPCLDVHGGR-----VVKG--------TNFVNLRDAGDPVELAAVYDKEGADEVV 48 Query: 340 FLNITGFRDFPLGDLPMIQVLRQTSKNVFVPLTVGGGIRDFTDASGRYYSSLEVAAEYFR 399 FL+IT D G M+ V+R+T++ VF+P TVGGG+R S+E E + Sbjct: 49 FLDITASSD---GRAIMLDVVRRTAEEVFIPFTVGGGLR-----------SVEDIREMLK 94 Query: 400 SGADKISIGSDAVSAAEEFIKSGVKTGKSSLEQISRVYGNQAVVVSIDPRRVYVNHPDDV 459 +GADKIS+ + AV + K +G+Q +VV+ID RR Sbjct: 95 AGADKISLNTSAVQTPKLISDGAWK------------FGSQCIVVAIDARR--------- 133 Query: 460 PYKVIRVTNPGPNGEEYAWYQCTVSGGREGRPIGAFELAKAVEELGAGEILLNCIDCDGQ 519 G ++ GGR+ I E A+ VEELGAGEILL +D DG Sbjct: 134 --------RRDAEGNPVEGWEVYTHGGRKPTGIDVLEWARRVEELGAGEILLTSMDKDGT 185 Query: 520 GKGFDIDLVKLISDSVGIPVIASSGAGTPDHFSEVFEKTNASAALAAGIFHRKEVPIQSV 579 G+DI L + +S++V IPVIAS G G DH E A AALAA IFH +E I Sbjct: 186 KDGYDIPLTRAVSEAVTIPVIASGGVGNLDHIVEGLTVGKADAALAASIFHYREYTIGET 245 Query: 580 KEHLQEERIEVR 591 KE+L+E + VR Sbjct: 246 KEYLRERGVHVR 257 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: 392 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: 261 Length adjustment: 31 Effective length of query: 561 Effective length of database: 230 Effective search space: 129030 Effective search space used: 129030 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