Align Imidazoleglycerol-phosphate dehydratase; IGPD; EC 4.2.1.19 (characterized)
to candidate WP_017600198.1 D471_RS0119675 imidazoleglycerol-phosphate dehydratase HisB
Query= SwissProt::P9WML9 (210 letters) >NCBI__GCF_000341125.1:WP_017600198.1 Length = 197 Score = 234 bits (596), Expect = 1e-66 Identities = 117/201 (58%), Positives = 145/201 (72%), Gaps = 5/201 (2%) Query: 10 SRRARIERRTRESDIVIELDLDGTGQVAVDTGVPFYDHMLTALGSHASFDLTVRATGDVE 69 SR R+ER T+E+ +++E+DLDGTG V TGV F+DHML L H FDLTVR GD+ Sbjct: 2 SRTGRVERTTKETKVLVEIDLDGTGVADVSTGVGFFDHMLDQLAKHGLFDLTVRTEGDLH 61 Query: 70 IEAHHTIEDTAIALGTALGQALGDKRGIRRFGDAFIPMDETLAHAAVDLSGRPYCVHTGE 129 I++HHT+EDTA+ALG A +ALGDKRGIRRF D +P+DE LA VD+SGRPY VH+ E Sbjct: 62 IDSHHTMEDTALALGAAFREALGDKRGIRRFADTKVPLDEALAEVTVDVSGRPYLVHS-E 120 Query: 130 PDHLQHTTIAGSSVPYHTVINRHVFESLAANARIALHVRVLYGRDPHHITEAQYKAVARA 189 P+ + I G Y T + RH+ ES A AR+ALHV V YGR+ HHI E Q+KA+ARA Sbjct: 121 PEGM--APIIGRD--YDTTMTRHILESFVAQARVALHVHVPYGRNAHHIVECQFKALARA 176 Query: 190 LRQAVEPDPRVSGVPSTKGAL 210 LR A E DPRV+ +PSTKGAL Sbjct: 177 LRAATENDPRVTDIPSTKGAL 197 Lambda K H 0.319 0.133 0.386 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: 172 Number of extensions: 7 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: 210 Length of database: 197 Length adjustment: 21 Effective length of query: 189 Effective length of database: 176 Effective search space: 33264 Effective search space used: 33264 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 Apr 10 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