Alignments for a candidate for hisN in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisN in Shewanella oneidensis MR-1

Align imidazoleglycerol-phosphate dehydratase / histidinol-phosphatase (EC 4.2.1.19; EC 3.1.3.15) (characterized)
to candidate 201228 SO2071 imidazoleglycerol-phosphate dehydratase/histidinol-phosphatase (NCBI ptt file)

Query= ecocyc::IMIDPHOSPHADEHYDHISTIDPHOSPHA-MONOMER
         (355 letters)



>FitnessBrowser__MR1:201228
          Length = 363

 Score =  450 bits (1157), Expect = e-131
 Identities = 217/355 (61%), Positives = 268/355 (75%)

Query: 1   MSQKYLFIDRDGTLISEPPSDFQVDRFDKLAFEPGVIPELLKLQKAGYKLVMITNQDGLG 60
           ++QK LFIDRDGTLI EP +D QVD   KL FEP VIP LL+LQKAG++LVM++NQDGLG
Sbjct: 9   VAQKILFIDRDGTLIEEPVTDKQVDNLAKLVFEPQVIPALLRLQKAGFRLVMVSNQDGLG 68

Query: 61  TQSFPQADFDGPHNLMMQIFTSQGVQFDEVLICPHLPADECDCRKPKVKLVERYLAEQAM 120
           T SFPQ DFD PHN+MMQI +SQGV+F++VLICPH   + C CRKPK+ LV+ +L +  +
Sbjct: 69  TPSFPQEDFDAPHNMMMQILSSQGVKFEDVLICPHFNDENCSCRKPKLGLVKDFLTQGFI 128

Query: 121 DRANSYVIGDRATDIQLAENMGITGLRYDRETLNWPMIGEQLTRRDRYAHVVRNTKETQI 180
           D   S VIGDR TD++L   MGI   +Y R +L W  I + L  + R A VVR TKET I
Sbjct: 129 DFTQSAVIGDRHTDVELGNAMGIISFQYQRGSLGWNAIADALLNKGRSATVVRTTKETDI 188

Query: 181 DVQVWLDREGGSKINTGVGFFDHMLDQIATHGGFRMEINVKGDLYIDDHHTVEDTGLALG 240
            V V LD      INTG+GFFDHMLDQIATHG F+ME+NV GDL IDDHH+VEDT LA+G
Sbjct: 189 RVTVDLDNASKGTINTGIGFFDHMLDQIATHGNFKMEVNVDGDLEIDDHHSVEDTALAIG 248

Query: 241 EALKIALGDKRGICRFGFVLPMDECLARCALDISGRPHLEYKAEFTYQRVGDLSTEMIEH 300
           +AL+ ALGDKRGI RFGF LPMDE    C LD+SGRP +++ A+F  ++VG+++TEM+ H
Sbjct: 249 DALRQALGDKRGIARFGFSLPMDEAKGECLLDLSGRPFIKFAAQFEREKVGEMATEMVPH 308

Query: 301 FFRSLSYTMGVTLHLKTKGKNDHHRVESLFKAFGRTLRQAIRVEGDTLPSSKGVL 355
           FFRS +  +  TLH+  +G NDHH+VE+LFK  GR LRQA++VEGD LPSSKGVL
Sbjct: 309 FFRSFADGLRCTLHVAAEGDNDHHKVEALFKVLGRALRQAVKVEGDVLPSSKGVL 363


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: 448
Number of extensions: 18
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: 355
Length of database: 363
Length adjustment: 29
Effective length of query: 326
Effective length of database: 334
Effective search space:   108884
Effective search space used:   108884
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 201228 SO2071 (imidazoleglycerol-phosphate dehydratase/histidinol-phosphatase (NCBI ptt file))
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.19884.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    1.7e-76  241.2   0.0    2.5e-76  240.7   0.0    1.2  1  lcl|FitnessBrowser__MR1:201228  SO2071 imidazoleglycerol-phospha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:201228  SO2071 imidazoleglycerol-phosphate dehydratase/histidinol-phosphatase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.7   0.0   2.5e-76   2.5e-76       1     160 [.      11     170 ..      11     171 .. 0.99

  Alignments for each domain:
  == domain 1  score: 240.7 bits;  conditional E-value: 2.5e-76
                       TIGR01261   1 qkilfidrdGtlieePksdfqvdaleklklekkvipallklkeagyklvlvtnqdGlGtesfPkedfdkphalmlqifk 79 
                                     qkilfidrdGtlieeP +d qvd+l kl +e++vipall+l++ag++lv+v+nqdGlGt+sfP+edfd ph++m+qi++
  lcl|FitnessBrowser__MR1:201228  11 QKILFIDRDGTLIEEPVTDKQVDNLAKLVFEPQVIPALLRLQKAGFRLVMVSNQDGLGTPSFPQEDFDAPHNMMMQILS 89 
                                     79***************************************************************************** PP

                       TIGR01261  80 seGivfddvlicphfledncacrkPkiklleeylkkekidkersyviGdretdlqlaenlgirglkykeeelnwkeiak 158
                                     s+G++f+dvlicphf+++nc+crkPk++l++++l +  id  +s+viGdr+td++l + +gi +++y++ +l+w+ ia+
  lcl|FitnessBrowser__MR1:201228  90 SQGVKFEDVLICPHFNDENCSCRKPKLGLVKDFLTQGFIDFTQSAVIGDRHTDVELGNAMGIISFQYQRGSLGWNAIAD 168
                                     *****************************************************************************99 PP

                       TIGR01261 159 el 160
                                      l
  lcl|FitnessBrowser__MR1:201228 169 AL 170
                                     87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (161 nodes)
Target sequences:                          1  (363 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 13.07
//
[ok]

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

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis