Align Imidazoleglycerol-phosphate dehydratase; Short=IGPD; EC 4.2.1.19 (characterized, see rationale)
to candidate WP_092481815.1 BM299_RS02165 imidazoleglycerol-phosphate dehydratase HisB
Query= uniprot:Q9HU41 (197 letters) >NCBI__GCF_900115975.1:WP_092481815.1 Length = 200 Score = 200 bits (509), Expect = 1e-56 Identities = 99/194 (51%), Positives = 125/194 (64%), Gaps = 1/194 (0%) Query: 4 RKASVARDTLETQIKVSIDLDGTGKARFDTGVPFLDHMMDQIARHGLIDLDIECKGDLHI 63 R A V R+T ET + V +++DG GK DTGVPFLDHM+D +H +DL I+ +GDL + Sbjct: 8 RIAQVNRETAETSVSVDLNVDGGGKPAIDTGVPFLDHMLDLFTKHSGLDLSIDARGDLQV 67 Query: 64 DDHHTVEDIGITLGQAFAKAIGDKKGIRRYGHAYVPLDEALSRVVIDFSGRPGLQMHVPF 123 D HHTVED+GI LGQA A+GDK+GI RYGH +P+DE L V +DFSGR L V Sbjct: 68 DAHHTVEDVGICLGQALKAALGDKRGIERYGHVLLPMDETLVAVALDFSGRGHLAFDVSL 127 Query: 124 TRASVGGFDVDLFMEFFQGFVNHAQVTLHIDNLRGHNTHHQIETVFKAFGRALRMAIELD 183 VG FD +L EF + F + +TLH+ + G NTHH IE VFK GRALR A + Sbjct: 128 PAGKVGDFDTELVEEFLRAFAANGAMTLHVRLMAGKNTHHIIEAVFKGLGRALRSAAVIK 187 Query: 184 ERMAGQMPSTKGCL 197 + G +PSTKG L Sbjct: 188 DPTGG-IPSTKGIL 200 Score = 29.6 bits (65), Expect = 4e-05 Identities = 22/91 (24%), Positives = 36/91 (39%), Gaps = 12/91 (13%) Query: 3 ERKASVARDTLETQIKVSIDLDGTGKARFDTGVP----------FLDHMMDQIARHGLID 52 ER V ET + V++D G G FD +P ++ + A +G + Sbjct: 95 ERYGHVLLPMDETLVAVALDFSGRGHLAFDVSLPAGKVGDFDTELVEEFLRAFAANGAMT 154 Query: 53 LDIECKGDLHIDDHHTVEDIGITLGQAFAKA 83 L + + HH +E + LG+A A Sbjct: 155 LHVRLMAGK--NTHHIIEAVFKGLGRALRSA 183 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: 164 Number of extensions: 11 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 197 Length of database: 200 Length adjustment: 20 Effective length of query: 177 Effective length of database: 180 Effective search space: 31860 Effective search space used: 31860 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 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