Align imidazoleglycerol-phosphate dehydratase / histidinol-phosphatase (EC 4.2.1.19; EC 3.1.3.15) (characterized)
to candidate 5209747 Shew_2200 imidazole glycerol-phosphate dehydratase/histidinol phosphatase (RefSeq)
Query= ecocyc::IMIDPHOSPHADEHYDHISTIDPHOSPHA-MONOMER (355 letters) >FitnessBrowser__PV4:5209747 Length = 356 Score = 476 bits (1225), Expect = e-139 Identities = 233/355 (65%), Positives = 279/355 (78%) Query: 1 MSQKYLFIDRDGTLISEPPSDFQVDRFDKLAFEPGVIPELLKLQKAGYKLVMITNQDGLG 60 M QK LFIDRDGTLI EP +D QVD KL FEP VIP LLKLQ AGY+LVM++NQDGLG Sbjct: 2 MKQKILFIDRDGTLIEEPVTDKQVDSLAKLVFEPQVIPALLKLQGAGYRLVMVSNQDGLG 61 Query: 61 TQSFPQADFDGPHNLMMQIFTSQGVQFDEVLICPHLPADECDCRKPKVKLVERYLAEQAM 120 T SFP+ DFD P N+MMQIF SQGV+FD+VLICPH + C CRKPK+ LV+ YL E + Sbjct: 62 TPSFPKDDFDAPQNMMMQIFNSQGVKFDDVLICPHFDDENCSCRKPKLGLVKAYLTEGRV 121 Query: 121 DRANSYVIGDRATDIQLAENMGITGLRYDRETLNWPMIGEQLTRRDRYAHVVRNTKETQI 180 D S VIGDR TD+ LAE MGITG++Y+R+TLNW I EQL +R A VVR TKET I Sbjct: 122 DFTQSAVIGDRETDLGLAEAMGITGIQYNRDTLNWDAIAEQLLGGNRVATVVRTTKETDI 181 Query: 181 DVQVWLDREGGSKINTGVGFFDHMLDQIATHGGFRMEINVKGDLYIDDHHTVEDTGLALG 240 V V LD + S INTG+GFFDHMLDQIATHG FR++++V GDL IDDHH+VEDT LA+G Sbjct: 182 KVTVDLDSQLKSSINTGIGFFDHMLDQIATHGNFRLDVSVDGDLEIDDHHSVEDTALAIG 241 Query: 241 EALKIALGDKRGICRFGFVLPMDECLARCALDISGRPHLEYKAEFTYQRVGDLSTEMIEH 300 +AL+ ALGDKRGI RFGF +PMDE A C LD+SGRP ++++ +F + VG+++TEM+ H Sbjct: 242 DALRQALGDKRGIARFGFSIPMDEASASCLLDLSGRPFIKFEGQFEREMVGEMATEMVPH 301 Query: 301 FFRSLSYTMGVTLHLKTKGKNDHHRVESLFKAFGRTLRQAIRVEGDTLPSSKGVL 355 FFRSL+ + TLHL T+G NDHH+VESLFK FGRTLRQA++VEGD LPSSKGVL Sbjct: 302 FFRSLADGLRCTLHLSTQGDNDHHKVESLFKVFGRTLRQAVKVEGDALPSSKGVL 356 Lambda K H 0.322 0.140 0.420 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: 465 Number of extensions: 15 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: 355 Length of database: 356 Length adjustment: 29 Effective length of query: 326 Effective length of database: 327 Effective search space: 106602 Effective search space used: 106602 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: 49 (23.5 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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