Align imidazole glycerol-phosphate synthase (EC 4.3.2.10) (characterized)
to candidate WP_011373705.1 SUDEN_RS10865 imidazole glycerol phosphate synthase cyclase subunit
Query= BRENDA::Q9SZ30 (592 letters) >NCBI__GCF_000012965.1:WP_011373705.1 Length = 252 Score = 163 bits (413), Expect = 7e-45 Identities = 112/312 (35%), Positives = 164/312 (52%), Gaps = 64/312 (20%) Query: 281 AKRVIACLDVRTNDKGDLVVTKGDQYDVREQSNENEVRNLGKPVDLAGQYYKDGADEISF 340 AKR+I CLDV+ D V KG N +R+ G PV++A +Y ++GADEI+F Sbjct: 5 AKRIIPCLDVK-----DGRVVKG--------VNFVGLRDAGDPVEVAKRYNQEGADEITF 51 Query: 341 LNITGFRDFPLGDLPMIQVLRQTSKNVFVPLTVGGGIRDFTDASGRYYSSLEVAAEYFRS 400 L+IT D ++ ++ Q ++ +F+PLTVGGGIR D Y L V Sbjct: 52 LDITASSD---NRDTIVDIVAQVAREIFIPLTVGGGIRKLEDI----YRLLNV------- 97 Query: 401 GADKISIGSDAVSAAEEFIKSGVKTGKSSLEQISRVYGNQAVVVSIDPRRVYVNHPDDVP 460 G DK+S+ S A+ + +++ ++ +G+Q +V +ID ++ Sbjct: 98 GCDKVSVNSAAIKRPQ------------LIDESAKRFGSQCIVTAIDVKKT--------- 136 Query: 461 YKVIRVTNPGPNGEEYAWYQCTVSGGREGRPIGAFELAKAVEELGAGEILLNCIDCDGQG 520 G+ Y Y ++GGR I A E AK V E G+GEILL +D DG Sbjct: 137 ------------GDRYNVY---LNGGRVDTGIDALEWAKEVVERGSGEILLTSMDADGTK 181 Query: 521 KGFDIDLVKLISDSVGIPVIASSGAGTPDHFSEVFEKTNASAALAAGIFHRKEVPIQSVK 580 GF++ + +LIS++V +PVIAS GAGT H E FE A AALAA IFH +E+ I +K Sbjct: 182 AGFELSITQLISEAVNVPVIASGGAGTMKHIKEAFEH-GADAALAATIFHYREIDIMDLK 240 Query: 581 EHLQEERIEVRI 592 +L + I VR+ Sbjct: 241 RYLHDNNIPVRL 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: 364 Number of extensions: 21 Number of successful extensions: 6 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