Align imidazole glycerol-phosphate synthase (EC 4.3.2.10) (characterized)
to candidate 3609190 Dshi_2576 imidazoleglycerol phosphate synthase, cyclase subunit (RefSeq)
Query= BRENDA::Q9SZ30 (592 letters) >FitnessBrowser__Dino:3609190 Length = 253 Score = 140 bits (354), Expect = 5e-38 Identities = 109/310 (35%), Positives = 147/310 (47%), Gaps = 62/310 (20%) Query: 283 RVIACLDVRTNDKGDLVVTKGDQYDVREQSNENEVRNLGKPVDLAGQYYKDGADEISFLN 342 RVI CLDV D V KG N ++ + G PV+ A Y GADE+ FL+ Sbjct: 5 RVIPCLDV-----ADGRVVKG--------VNFVDLVDAGDPVESAKAYDAAGADELCFLD 51 Query: 343 ITGFRDFPLGDLPMIQVLRQTSKNVFVPLTVGGGIRDFTDASGRYYSSLEVAAEYFRSGA 402 I + M + +T++ F+PLT+GGG+R D +GA Sbjct: 52 IHATNE---NRGTMYDLATRTAEQCFMPLTIGGGVRTTEDVRN-----------LLLAGA 97 Query: 403 DKISIGSDAVSAAEEFIKSGVKTGKSSLEQISRVYGNQAVVVSIDPRRVYVNHPDDVPYK 462 DK+S S AV+ + ++ K +G+Q +V +ID + V Sbjct: 98 DKVSFNSAAVADPDVIARAADK------------FGSQCIVCAIDAKTVA---------- 135 Query: 463 VIRVTNPGPNGEEYAWYQCTVSGGREGRPIGAFELAKAVEELGAGEILLNCIDCDGQGKG 522 PG ++ GGR+ I A E AK V E GAGEILL +D DG +G Sbjct: 136 ------PGR-------WEIFTHGGRKPTGIDAVEFAKTVVEKGAGEILLTSMDRDGTKQG 182 Query: 523 FDIDLVKLISDSVGIPVIASSGAGTPDHFSEVFEKTNASAALAAGIFHRKEVPIQSVKEH 582 F+I L + ISD+V +PVIAS G GT DH E + ASA LAA IFH E I+ KEH Sbjct: 183 FNIALTRAISDAVSVPVIASGGVGTLDHLVEGVTEGGASAVLAASIFHFGEFTIREAKEH 242 Query: 583 LQEERIEVRI 592 + E I VR+ Sbjct: 243 MAEAGIPVRL 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: 332 Number of extensions: 19 Number of successful extensions: 4 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: 253 Length adjustment: 30 Effective length of query: 562 Effective length of database: 223 Effective search space: 125326 Effective search space used: 125326 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