Align Imidazoleglycerol-phosphate dehydratase; Short=IGPD; EC 4.2.1.19 (characterized, see rationale)
to candidate 206474 DVU1040 imidazoleglycerol-phosphate dehydratase
Query= uniprot:Q9HU41 (197 letters) >MicrobesOnline__882:206474 Length = 202 Score = 163 bits (412), Expect = 2e-45 Identities = 88/195 (45%), Positives = 118/195 (60%), Gaps = 4/195 (2%) Query: 4 RKASVARDTLETQIKVSIDLDGTGKARFDTGVPFLDHMMDQIARHGLIDLDIECKGDLHI 63 RKASV R T ET I +++ ++G G R TG LDHM+ A DLD+ CKGD+HI Sbjct: 10 RKASVERVTNETTIALTLTIEGEGNVRVTTGFGMLDHMLTLTAFWAGFDLDLTCKGDMHI 69 Query: 64 DDHHTVEDIGITLGQAFAKAIGDKKGIRRYGHAYVPLDEALSRVVIDFSGRPGLQMH-VP 122 D HHT ED+ + LGQA A A+ D+KGI R G A VP+DEAL+ V +D SGRP L+ Sbjct: 70 DAHHTAEDVALCLGQALATALDDRKGIARVGFARVPMDEALAEVTLDISGRPWLEWRGDE 129 Query: 123 FTRASVGGFDVDLFMEFFQGFVNHAQVTLHIDNLRGHNTHHQIETVFKAFGRALRMAIEL 182 + + G + DL+ EF + F + A++ LH+ L G N HH +E+ K G ALR A+ Sbjct: 130 YLPPVIAGEEKDLWREFHKAFASAARMNLHVSYLYGKNGHHLLESASKGLGLALRQAVRR 189 Query: 183 DERMAGQMPSTKGCL 197 D + + STKG L Sbjct: 190 DRQ---TVLSTKGSL 201 Lambda K H 0.325 0.141 0.421 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: 149 Number of extensions: 9 Number of successful extensions: 3 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: 197 Length of database: 202 Length adjustment: 21 Effective length of query: 176 Effective length of database: 181 Effective search space: 31856 Effective search space used: 31856 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 45 (21.9 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