Align Imidazole glycerol phosphate synthase subunit HisH; EC 4.3.2.10; IGP synthase glutaminase subunit; EC 3.5.1.2; IGP synthase subunit HisH; ImGP synthase subunit HisH; IGPS subunit HisH (uncharacterized)
to candidate WP_010526802.1 GQW_RS0104315 type 1 glutamine amidotransferase
Query= curated2:P58789 (194 letters) >NCBI__GCF_000220155.1:WP_010526802.1 Length = 236 Score = 45.8 bits (107), Expect = 6e-10 Identities = 41/142 (28%), Positives = 62/142 (43%), Gaps = 22/142 (15%) Query: 53 LAPIKDIIIEGINEGKPFLGICLGMQLLFEESEESPGKEGLGIFKGKVVKLKNVRTPHIG 112 LA K I E I+ GK LGICLG QL+ KV K P IG Sbjct: 68 LAEEKKAIKEAIDRGKTVLGICLGSQLI------------AATLGAKVTKNPE---PEIG 112 Query: 113 WNQVWIKKECKLFEGLKNGSYFYFVHSYHA----VPQDPDIIATTTDYENAEFVSSVCFE 168 W V + + K KN + + +H +P +AT+ +N FV + Sbjct: 113 WFDVTLTDQGKQNPLFKNIENTFKIFQWHGDTFEIPAGALHLATSPVCKNQAFVFG---D 169 Query: 169 NIFGVQFHPEKSSKNGLILLRN 190 + G+QFH E ++++ ++LR+ Sbjct: 170 RVLGLQFHLEVTNESLNLMLRD 191 Lambda K H 0.320 0.142 0.427 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: 135 Number of extensions: 6 Number of successful extensions: 2 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: 194 Length of database: 236 Length adjustment: 22 Effective length of query: 172 Effective length of database: 214 Effective search space: 36808 Effective search space used: 36808 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 (21.8 bits) S2: 45 (21.9 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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