GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN 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)

Align candidate 5209747 Shew_2200 (imidazole glycerol-phosphate dehydratase/histidinol phosphatase (RefSeq))
to HMM TIGR01261 (hisB: histidinol-phosphatase (EC 3.1.3.15))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01261.hmm
# target sequence database:        /tmp/gapView.25114.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01261  [M=161]
Accession:   TIGR01261
Description: hisB_Nterm: histidinol-phosphatase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
    8.4e-81  255.3   0.0    1.2e-80  254.7   0.0    1.2  1  lcl|FitnessBrowser__PV4:5209747  Shew_2200 imidazole glycerol-pho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209747  Shew_2200 imidazole glycerol-phosphate dehydratase/histidinol phosphatase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  254.7   0.0   1.2e-80   1.2e-80       1     160 [.       4     163 ..       4     164 .. 0.99

  Alignments for each domain:
  == domain 1  score: 254.7 bits;  conditional E-value: 1.2e-80
                        TIGR01261   1 qkilfidrdGtlieePksdfqvdaleklklekkvipallklkeagyklvlvtnqdGlGtesfPkedfdkphalmlqif 78 
                                      qkilfidrdGtlieeP +d qvd+l kl +e++vipallkl+ agy+lv+v+nqdGlGt+sfPk+dfd p+++m+qif
  lcl|FitnessBrowser__PV4:5209747   4 QKILFIDRDGTLIEEPVTDKQVDSLAKLVFEPQVIPALLKLQGAGYRLVMVSNQDGLGTPSFPKDDFDAPQNMMMQIF 81 
                                      79**************************************************************************** PP

                        TIGR01261  79 kseGivfddvlicphfledncacrkPkiklleeylkkekidkersyviGdretdlqlaenlgirglkykeeelnwkei 156
                                      +s+G++fddvlicphf ++nc+crkPk++l+++yl + ++d  +s+viGdretdl lae +gi+g++y++++lnw+ i
  lcl|FitnessBrowser__PV4:5209747  82 NSQGVKFDDVLICPHFDDENCSCRKPKLGLVKAYLTEGRVDFTQSAVIGDRETDLGLAEAMGITGIQYNRDTLNWDAI 159
                                      ****************************************************************************** PP

                        TIGR01261 157 akel 160
                                      a++l
  lcl|FitnessBrowser__PV4:5209747 160 AEQL 163
                                      *998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (161 nodes)
Target sequences:                          1  (356 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 9.95
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Links

Downloads

Related tools

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