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::A4WHB6 (251 letters) >FitnessBrowser__Caulo:CCNA_03852 Length = 244 Score = 112 bits (281), Expect = 5e-30 Identities = 72/227 (31%), Positives = 122/227 (53%), Gaps = 10/227 (4%) Query: 7 PCLDM-DGKAGVVVKGVNFEGVREVGDPVEMAVRYEEEGADEIAILDITATPEGRSTFVE 65 P +D+ DG+ ++ G + P + A R+ ++G + ++D+ EG+S Sbjct: 8 PAIDLKDGQCVRLLHGDMDKATVFNTSPADQAQRFVQDGFSWLHVVDLNGAIEGKSVNTA 67 Query: 66 SVRRVAEAVSIPVLVGGGVRGIEDAAALFKAGADKVSVNTAAVKNPRLVSEIAREFGSQS 125 +V ++ E++SIPV +GGG+R +E A +AG +V + T AV +P LV + AR + Q Sbjct: 68 AVEQILESISIPVQLGGGIRTLEGVEAWIEAGVSRVILGTVAVHDPELVKKAARLWPEQ- 126 Query: 126 TVVAIDAKLVGGRYEVFVRGGKEPTGLDAVEWAKKVEELGAGEILLTSIDKDGTRLGYDV 185 VA+D + +V V G + L A++ +++ E+ G +++T I +DG G +V Sbjct: 127 IAVAVDVR----DGKVAVDGWTGLSDLSAIDLSRRFEDAGVAALIITDISRDGALTGVNV 182 Query: 186 ELIRRVAEAVKIPVIASGGAGALEHFYEAAAAG----ADAVLAASLF 228 E + +A+AV IPVIASGG A+ A A A+L SL+ Sbjct: 183 EGVGELADAVSIPVIASGGVAAVADIERLKARQGVEIAGAILGRSLY 229 Lambda K H 0.318 0.136 0.375 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: 155 Number of extensions: 10 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: 251 Length of database: 244 Length adjustment: 24 Effective length of query: 227 Effective length of database: 220 Effective search space: 49940 Effective search space used: 49940 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 (21.7 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