Align imidazole glycerol-phosphate synthase (EC 4.3.2.10) (characterized)
to candidate WP_011020590.1 MA_RS02840 imidazole glycerol phosphate synthase cyclase subunit
Query= BRENDA::Q9SZ30 (592 letters) >NCBI__GCF_000007345.1:WP_011020590.1 Length = 273 Score = 192 bits (488), Expect = 1e-53 Identities = 125/315 (39%), Positives = 172/315 (54%), Gaps = 45/315 (14%) Query: 280 LAKRVIACLDVRTNDKGDLVVTKGDQYDVREQSNENEVRNLGKPVDLAGQYYKDGADEIS 339 L KR+I CLDV + G VV + D++E G PV+LA +Y +DGADE+ Sbjct: 2 LTKRIIPCLDVTLDRAGGCVVKGVEFVDLKEA---------GDPVELAKRYNEDGADELV 52 Query: 340 FLNITGFRDFPLGDLPMIQVLRQTSKNVFVPLTVGGGIRDFTDASGRYYSSLEVAAEYFR 399 FL+IT G MI V+ +T+ VF+PLTVGGGI SS++ + R Sbjct: 53 FLDITASAH---GRETMIDVIERTADEVFIPLTVGGGI-----------SSIDAIRQILR 98 Query: 400 SGADKISIGSDAVSAAEEFIKSGVKTGKSSLEQISRVYGNQAVVVSIDPRRV--YVNHPD 457 +GADK+S+ + AV + FIK S ++G Q +V +ID RR N+PD Sbjct: 99 AGADKVSVNTSAVKNPD-FIKES-----------SDIFGAQCIVTAIDCRRNTDIKNNPD 146 Query: 458 DVPYKVIRVTNPGPNGEEYAWYQCTVSGGREGRPIGAFELAKAVEELGAGEILLNCIDCD 517 V+ + + P AWY+ + GGRE I A + AK EELG+GEILL +D D Sbjct: 147 KT---VLELEDGTP-----AWYEVVIYGGREATGIDAVQWAKKAEELGSGEILLTSMDRD 198 Query: 518 GQGKGFDIDLVKLISDSVGIPVIASSGAGTPDHFSEVFEKTNASAALAAGIFHRKEVPIQ 577 G G+D+ + + +S+ + IP+IAS G G P H E F + A AALAA IFH E I Sbjct: 199 GTCAGYDLPITRKLSEELDIPIIASGGVGNPQHIYEGFSEGKADAALAASIFHFSEYSIW 258 Query: 578 SVKEHLQEERIEVRI 592 VKE+L+E I VR+ Sbjct: 259 EVKEYLREREIPVRL 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: 395 Number of extensions: 22 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: 273 Length adjustment: 31 Effective length of query: 561 Effective length of database: 242 Effective search space: 135762 Effective search space used: 135762 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