Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate AZOBR_RS01680 AZOBR_RS01680 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
Query= BRENDA::A4WHB6 (251 letters) >FitnessBrowser__azobra:AZOBR_RS01680 Length = 249 Score = 99.8 bits (247), Expect = 5e-26 Identities = 63/206 (30%), Positives = 109/206 (52%), Gaps = 6/206 (2%) Query: 5 VIPCLDM-DGKAGVVVKGVNFEGVREVGDPVEMAVRYEEEGADEIAILDITATPEGRSTF 63 + P +D+ DG +++G + +P + A +E +G + + ++D+ EG+ Sbjct: 3 IYPAIDLKDGACVRLLRGEMSQATVFNTEPADQARLFESQGFEWLHLVDLNGAFEGKPVN 62 Query: 64 VESVRRVAEAVSIPVLVGGGVRGIEDAAALFKAGADKVSVNTAAVKNPRLVSEIAREFGS 123 ++V + AV+IPV +GGG+R ++ A + G +V + T A++ P LV E REF Sbjct: 63 GKAVESILGAVAIPVQLGGGIRDLKTIAHWLEKGVSRVILGTVALREPELVREACREFPG 122 Query: 124 QSTVVAIDAKLVGGRYEVFVRGGKEPTGLDAVEWAKKVEELGAGEILLTSIDKDGTRLGY 183 + V IDA+ V V G E + + A++ A K E+ G I+ T I++DG G Sbjct: 123 K-VAVGIDAR----EGYVAVAGWAETSTIKALDLALKFEDSGVAAIIYTDINRDGAMGGV 177 Query: 184 DVELIRRVAEAVKIPVIASGGAGALE 209 +VE +A + PVIASGG +++ Sbjct: 178 NVEATSDLAFHLTTPVIASGGVSSID 203 Score = 35.0 bits (79), Expect = 1e-06 Identities = 19/62 (30%), Positives = 32/62 (51%) Query: 34 VEMAVRYEEEGADEIAILDITATPEGRSTFVESVRRVAEAVSIPVLVGGGVRGIEDAAAL 93 +++A+++E+ G I DI VE+ +A ++ PV+ GGV I+D AL Sbjct: 149 LDLALKFEDSGVAAIIYTDINRDGAMGGVNVEATSDLAFHLTTPVIASGGVSSIDDLIAL 208 Query: 94 FK 95 K Sbjct: 209 KK 210 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: 156 Number of extensions: 9 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: 251 Length of database: 249 Length adjustment: 24 Effective length of query: 227 Effective length of database: 225 Effective search space: 51075 Effective search space used: 51075 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