Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate WP_083536455.1 ACG33_RS15635 imidazole glycerol phosphate synthase subunit HisF
Query= BRENDA::Q8ZY16 (253 letters) >NCBI__GCF_001579945.1:WP_083536455.1 Length = 255 Score = 169 bits (427), Expect = 7e-47 Identities = 93/229 (40%), Positives = 140/229 (61%), Gaps = 5/229 (2%) Query: 6 RIIPCLDIDGKAGVVVKGVNFQGIREVGDPVEMAVRYEEEGADEIAILDITAAPEGRATF 65 R+IPCL + G ++K F+ R VGD + + ++ DE+ +LDI A G Sbjct: 5 RVIPCLLLTGSG--LIKTRRFRHRRYVGDIINAVRIFNDKEVDELLVLDIDATIVGYEPR 62 Query: 66 IDSVKRVAEAVSIPVLVGGGVRSLEDATTLFRAGADKVSVNTAAVRNPQLVALLAREFGS 125 +D + +A +P+ GGG+ S++ A LF AG +KV VN+AA+R P+L+ ++ FGS Sbjct: 63 LDIITSIAGECFMPLAYGGGISSMKQAEELFTAGVEKVVVNSAAIRQPELIKQVSSNFGS 122 Query: 126 QSTVVAIDAK--WNGEYYEVYVKGGREATGLDAVKWAKEVEELGAGEILLTSIDRDGTGL 183 QS VV ID K W G + Y++ GR+ TG+ ++ A VE GAGEI++ SI+RDG + Sbjct: 123 QSVVVCIDYKRNWLGRVH-TYIESGRKCTGMTPLEHAGYVEAQGAGEIIIQSIERDGCRM 181 Query: 184 GYDVELIRRVADSVRIPVIASGGAGRVEHFYEAAAAGADAVLAASLFHF 232 GYD++LIR++A + +P+IA GGA ++ F A GA AV A S+F F Sbjct: 182 GYDLDLIRQIASATNVPLIACGGAHQLTDFSAAIDRGASAVSAGSMFVF 230 Score = 39.3 bits (90), Expect = 8e-08 Identities = 25/85 (29%), Positives = 41/85 (48%) Query: 35 PVEMAVRYEEEGADEIAILDITAAPEGRATFIDSVKRVAEAVSIPVLVGGGVRSLEDATT 94 P+E A E +GA EI I I +D ++++A A ++P++ GG L D + Sbjct: 154 PLEHAGYVEAQGAGEIIIQSIERDGCRMGYDLDLIRQIASATNVPLIACGGAHQLTDFSA 213 Query: 95 LFRAGADKVSVNTAAVRNPQLVALL 119 GA VS + V + + A+L Sbjct: 214 AIDRGASAVSAGSMFVFHGKHQAVL 238 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: 168 Number of extensions: 12 Number of successful extensions: 4 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: 255 Length adjustment: 24 Effective length of query: 229 Effective length of database: 231 Effective search space: 52899 Effective search space used: 52899 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: 47 (22.7 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