Align Imidazole glycerol phosphate synthase subunit HisH; IGP synthase glutaminase subunit; IGP synthase subunit HisH; ImGP synthase subunit HisH; IGPS subunit HisH; EC 4.3.2.10; EC 3.5.1.2 (characterized)
to candidate 7026133 Shewana3_3275 cobyric acid synthase (RefSeq)
Query= SwissProt::Q7SIC0 (200 letters) >FitnessBrowser__ANA3:7026133 Length = 541 Score = 45.4 bits (106), Expect = 2e-09 Identities = 28/72 (38%), Positives = 41/72 (56%), Gaps = 7/72 (9%) Query: 41 ADLLVLPGQGHFGQVMRAFQESGFVERVRRHLERGLPFLGICVGMQVLYE------GSEE 94 ADLL+LPG + + +E G+ +++ +HL G LGIC G Q+L E G E+ Sbjct: 330 ADLLILPGSKNVRADLAFLREQGWDKQIAKHLRYGGKLLGICGGYQMLGESIADPMGIED 389 Query: 95 APGV-RGLGLVP 105 GV +GLG +P Sbjct: 390 TLGVSQGLGYLP 401 Lambda K H 0.322 0.141 0.425 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: 244 Number of extensions: 14 Number of successful extensions: 1 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: 200 Length of database: 541 Length adjustment: 28 Effective length of query: 172 Effective length of database: 513 Effective search space: 88236 Effective search space used: 88236 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: 48 (23.1 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