Align Imidazole glycerol phosphate synthase subunit HisF; IGP synthase cyclase subunit; IGP synthase subunit HisF; ImGP synthase subunit HisF; IGPS subunit HisF; EC 4.3.2.10 (characterized)
to candidate AO356_03380 AO356_03380 glycosyl amidation-associated protein WbuZ
Query= SwissProt::Q7SIB9 (252 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_03380 Length = 253 Score = 167 bits (423), Expect = 2e-46 Identities = 95/229 (41%), Positives = 141/229 (61%), Gaps = 4/229 (1%) Query: 5 KRIVPCLDVHAGRVVKGVNFVNLRDAGDPVEAARAYDEAGADELVFLDISATHEERAILL 64 KR++PCL + +VK V F + + GDPV A R ++E DELV LDI A+ R Sbjct: 4 KRVIPCLLLKDRGLVKTVKFKSPKYVGDPVNAIRIFNEKEVDELVLLDIEASILGREPDY 63 Query: 65 DVVARVAERVFIPLTVGGGVRSLEDARKLLLSGADKVSVNSAAVRRPELIRELADHFGAQ 124 +++A VA F+P+ GGG+R+LE A+++ G +K+++N+AA+ EL+R++AD FG+Q Sbjct: 64 ELLAEVAGECFMPICYGGGIRTLEHAQRVFALGVEKIALNTAALADVELLRKIADQFGSQ 123 Query: 125 AVVLAIDAR--WRGDFPEVHVAGGRVPTGLHAVEWAVKGVELGAGEILLTSMDRDGTKEG 182 +VV +ID + G + V+ G T + VEWA + + GAGEI L S+DRDGT +G Sbjct: 124 SVVCSIDCKKSLLGRY-SVYSQSGTKDTKVSPVEWAKRVEDAGAGEIFLNSIDRDGTMQG 182 Query: 183 YDLRLTRMVAEAVGVPVIASGGAGRMEHFLEAFQ-AGAEAALAASVFHF 230 +D+ L + V V +PV+A GGAG + E F+ AG A A S F F Sbjct: 183 FDIPLIKSVVAGVHIPVVACGGAGSIADLNEPFEKAGVSAVAAGSFFVF 231 Lambda K H 0.321 0.138 0.398 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: 174 Number of extensions: 8 Number of successful extensions: 4 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: 252 Length of database: 253 Length adjustment: 24 Effective length of query: 228 Effective length of database: 229 Effective search space: 52212 Effective search space used: 52212 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 (21.9 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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