Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate GFF1767 PGA1_c17910 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase-like protein
Query= BRENDA::Q8ZY16 (253 letters) >FitnessBrowser__Phaeo:GFF1767 Length = 247 Score = 77.0 bits (188), Expect = 3e-19 Identities = 60/202 (29%), Positives = 98/202 (48%), Gaps = 7/202 (3%) Query: 5 LRIIPCLDI-DGKAGVVVKGVNFQGIREVGDPVEMAVRYEEEGADEIAILDITAAPEGRA 63 + I P +++ DG+ + KG + DPV A + +GA+ + + D A EG Sbjct: 1 MMIYPTMELKDGRCVTLDKGRLDTAMVWHVDPVATACSFAADGAEWMHLTDFDAI-EGDN 59 Query: 64 TFIDSVKRVAEAVSIPVLVGGGVRSLEDATTLFRAGADKVSVNTAAVRNPQLVALLAREF 123 V+ + IPV +GGG+RS E GA +V V T A ++P++V +L R + Sbjct: 60 RNAGLVEEIIRTAGIPVQLGGGMRSREHVEHWIDKGAGRVVVGTLAAQDPEMVRMLTRLY 119 Query: 124 GSQSTVVAIDAKWNGEYYEVYVKGGREATGLDAVKWAKEVEELGAGEILLTSIDRDGTGL 183 Q V+A+D W G +V G R+A + + + I++T I+ D + + Sbjct: 120 PDQ-IVLAVDV-WEG---QVMTDGWRQAGSFTPEAFIEAFADCPFAGIIITDIESDMSDV 174 Query: 184 GYDVELIRRVADSVRIPVIASG 205 + LI +A+ R PVIASG Sbjct: 175 EAQLGLIAGLAEKARTPVIASG 196 Score = 22.3 bits (46), Expect = 0.010 Identities = 17/55 (30%), Positives = 22/55 (40%), Gaps = 4/55 (7%) Query: 175 SIDRDGTGLGYDVELIRRVADSVRIPVIASGGAGRVEHFYEAAAAGADAVLAASL 229 +I+ D G E+IR IPV GG EH GA V+ +L Sbjct: 54 AIEGDNRNAGLVEEIIRTAG----IPVQLGGGMRSREHVEHWIDKGAGRVVVGTL 104 Lambda K H 0.318 0.137 0.381 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: 139 Number of extensions: 8 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 253 Length of database: 247 Length adjustment: 24 Effective length of query: 229 Effective length of database: 223 Effective search space: 51067 Effective search space used: 51067 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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