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_245577071.1 H589_RS0107915 aminodeoxychorismate/anthranilate synthase component II
Query= curated2:Q88UE1 (208 letters) >NCBI__GCF_000425265.1:WP_245577071.1 Length = 189 Score = 37.0 bits (84), Expect = 2e-07 Identities = 33/121 (27%), Positives = 51/121 (42%), Gaps = 29/121 (23%) Query: 66 QALARSGKPVLGICLGMQLLFESSSEYGEHAGL-GLLSGRVSALPTDLNVKVPQMGWNQN 124 +A+ +SGKPVLG+CLGMQ++ E G+ + L G GR K+ G N Sbjct: 72 EAVIKSGKPVLGVCLGMQIINEYCG--GKTSRLKGCFHGRTE--------KISFAGLQLN 121 Query: 125 ELRRPDSPFASIDAAYTYFVHSYYA--VCPATEIVATVQHGVQVPSIVQQQNVIGMQFHP 182 R HS + + E+++ G+ + ++G QFHP Sbjct: 122 VAR----------------YHSLFCSEIGDGLEVISENNEGIPMAVSHGSLPLLGYQFHP 165 Query: 183 E 183 E Sbjct: 166 E 166 Lambda K H 0.319 0.133 0.380 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: 97 Number of extensions: 9 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 208 Length of database: 189 Length adjustment: 20 Effective length of query: 188 Effective length of database: 169 Effective search space: 31772 Effective search space used: 31772 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 25 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