Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate CCNA_03852 CCNA_03852 phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide isomerase
Query= BRENDA::Q8ZY16 (253 letters) >FitnessBrowser__Caulo:CCNA_03852 Length = 244 Score = 111 bits (278), Expect = 1e-29 Identities = 73/229 (31%), Positives = 121/229 (52%), Gaps = 10/229 (4%) Query: 7 IIPCLDI-DGKAGVVVKGVNFQGIREVGDPVEMAVRYEEEGADEIAILDITAAPEGRATF 65 + P +D+ DG+ ++ G + P + A R+ ++G + ++D+ A EG++ Sbjct: 6 LYPAIDLKDGQCVRLLHGDMDKATVFNTSPADQAQRFVQDGFSWLHVVDLNGAIEGKSVN 65 Query: 66 IDSVKRVAEAVSIPVLVGGGVRSLEDATTLFRAGADKVSVNTAAVRNPQLVALLAREFGS 125 +V+++ E++SIPV +GGG+R+LE AG +V + T AV +P+LV AR + Sbjct: 66 TAAVEQILESISIPVQLGGGIRTLEGVEAWIEAGVSRVILGTVAVHDPELVKKAARLWPE 125 Query: 126 QSTVVAIDAKWNGEYYEVYVKGGREATGLDAVKWAKEVEELGAGEILLTSIDRDGTGLGY 185 Q VA+D + +V V G + L A+ ++ E+ G +++T I RDG G Sbjct: 126 Q-IAVAVDVRDG----KVAVDGWTGLSDLSAIDLSRRFEDAGVAALIITDISRDGALTGV 180 Query: 186 DVELIRRVADSVRIPVIASGGAGRVEHFYEAAAAG----ADAVLAASLF 230 +VE + +AD+V IPVIASGG V A A A+L SL+ Sbjct: 181 NVEGVGELADAVSIPVIASGGVAAVADIERLKARQGVEIAGAILGRSLY 229 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: 160 Number of extensions: 9 Number of successful extensions: 5 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: 253 Length of database: 244 Length adjustment: 24 Effective length of query: 229 Effective length of database: 220 Effective search space: 50380 Effective search space used: 50380 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