Align imidazole glycerol-phosphate synthase (EC 4.3.2.10) (characterized)
to candidate 209220 DVU0286 imidazoleglycerol phosphate synthase, cyclase subunit
Query= BRENDA::Q9SZ30 (592 letters) >MicrobesOnline__882:209220 Length = 259 Score = 144 bits (364), Expect = 3e-39 Identities = 102/314 (32%), Positives = 158/314 (50%), Gaps = 59/314 (18%) Query: 280 LAKRVIACLDVRTNDKGDLVVTKGDQYDVREQSNENEVRNLGKPVDLAGQYYKDGADEIS 339 L+KR+I CLDVR +TKG ++ E V ++G PV A +YY++GADEI Sbjct: 2 LSKRIIPCLDVRAGR-----LTKGVKF-------EGNV-DIGDPVATARRYYEEGADEIV 48 Query: 340 FLNITGFRDFPLGDLPM-IQVLRQTSKNVFVPLTVGGGIRDFTDASGRYYSSLEVAAEYF 398 F +IT + D + + V+ + + +F+P +VGGGI D Sbjct: 49 FYDITASHE----DRGIFLDVVERVASEIFIPFSVGGGINTVDDMRA-----------VL 93 Query: 399 RSGADKISIGSDAVSAAEEFIKSGVKTGKSSLEQISRVYGNQAVVVSIDPRRVYVNHPDD 458 +GA+K+S+ S AV + + Q + +G+QA+VV +D ++V Sbjct: 94 MAGAEKVSVNSGAVKTPD------------IISQGAAAFGSQAIVVGMDVKQV------- 134 Query: 459 VPYKVIRVTNPGPNGEEYAWYQCTVSGGREGRPIGAFELAKAVEELGAGEILLNCIDCDG 518 + P+G Y+ + GGR+ + A E AK E LGAGE+ +N ID DG Sbjct: 135 ------EKSATIPSG-----YEIVIHGGRKYMGMDAIEWAKTCESLGAGELCVNSIDADG 183 Query: 519 QGKGFDIDLVKLISDSVGIPVIASSGAGTPDHFSEVFEKTNASAALAAGIFHRKEVPIQS 578 G+++ L ++ISD+V IPVIAS GAG+P+H + + ASAAL A I H I Sbjct: 184 TKDGYELTLTRMISDAVTIPVIASGGAGSPEHMYDALTRGGASAALIASIVHYGTYTIPD 243 Query: 579 VKEHLQEERIEVRI 592 +K + ++R+ Sbjct: 244 LKRRISGMGAKMRM 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: 373 Number of extensions: 22 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: 259 Length adjustment: 30 Effective length of query: 562 Effective length of database: 229 Effective search space: 128698 Effective search space used: 128698 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