GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisB in Shewanella loihica PV-4

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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