Alignments for a candidate for hisN in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisN in Escherichia coli BW25113

Align imidazoleglycerol-phosphate dehydratase / histidinol-phosphatase (EC 4.2.1.19; EC 3.1.3.15) (characterized)
to candidate 16130 b2022 imidazoleglycerolphosphate dehydratase and histidinol-phosphate phosphatase (VIMSS)

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



>FitnessBrowser__Keio:16130
          Length = 355

 Score =  724 bits (1870), Expect = 0.0
 Identities = 355/355 (100%), Positives = 355/355 (100%)

Query: 1   MSQKYLFIDRDGTLISEPPSDFQVDRFDKLAFEPGVIPELLKLQKAGYKLVMITNQDGLG 60
           MSQKYLFIDRDGTLISEPPSDFQVDRFDKLAFEPGVIPELLKLQKAGYKLVMITNQDGLG
Sbjct: 1   MSQKYLFIDRDGTLISEPPSDFQVDRFDKLAFEPGVIPELLKLQKAGYKLVMITNQDGLG 60

Query: 61  TQSFPQADFDGPHNLMMQIFTSQGVQFDEVLICPHLPADECDCRKPKVKLVERYLAEQAM 120
           TQSFPQADFDGPHNLMMQIFTSQGVQFDEVLICPHLPADECDCRKPKVKLVERYLAEQAM
Sbjct: 61  TQSFPQADFDGPHNLMMQIFTSQGVQFDEVLICPHLPADECDCRKPKVKLVERYLAEQAM 120

Query: 121 DRANSYVIGDRATDIQLAENMGITGLRYDRETLNWPMIGEQLTRRDRYAHVVRNTKETQI 180
           DRANSYVIGDRATDIQLAENMGITGLRYDRETLNWPMIGEQLTRRDRYAHVVRNTKETQI
Sbjct: 121 DRANSYVIGDRATDIQLAENMGITGLRYDRETLNWPMIGEQLTRRDRYAHVVRNTKETQI 180

Query: 181 DVQVWLDREGGSKINTGVGFFDHMLDQIATHGGFRMEINVKGDLYIDDHHTVEDTGLALG 240
           DVQVWLDREGGSKINTGVGFFDHMLDQIATHGGFRMEINVKGDLYIDDHHTVEDTGLALG
Sbjct: 181 DVQVWLDREGGSKINTGVGFFDHMLDQIATHGGFRMEINVKGDLYIDDHHTVEDTGLALG 240

Query: 241 EALKIALGDKRGICRFGFVLPMDECLARCALDISGRPHLEYKAEFTYQRVGDLSTEMIEH 300
           EALKIALGDKRGICRFGFVLPMDECLARCALDISGRPHLEYKAEFTYQRVGDLSTEMIEH
Sbjct: 241 EALKIALGDKRGICRFGFVLPMDECLARCALDISGRPHLEYKAEFTYQRVGDLSTEMIEH 300

Query: 301 FFRSLSYTMGVTLHLKTKGKNDHHRVESLFKAFGRTLRQAIRVEGDTLPSSKGVL 355
           FFRSLSYTMGVTLHLKTKGKNDHHRVESLFKAFGRTLRQAIRVEGDTLPSSKGVL
Sbjct: 301 FFRSLSYTMGVTLHLKTKGKNDHHRVESLFKAFGRTLRQAIRVEGDTLPSSKGVL 355


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: 637
Number of extensions: 15
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: 355
Length adjustment: 29
Effective length of query: 326
Effective length of database: 326
Effective search space:   106276
Effective search space used:   106276
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 16130 b2022 (imidazoleglycerolphosphate dehydratase and histidinol-phosphate phosphatase (VIMSS))
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.8720.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    6.1e-88  278.5   0.0    8.7e-88  278.0   0.0    1.2  1  lcl|FitnessBrowser__Keio:16130  b2022 imidazoleglycerolphosphate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:16130  b2022 imidazoleglycerolphosphate dehydratase and histidinol-phosphate phosphatase (VI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.0   0.0   8.7e-88   8.7e-88       1     160 [.       3     162 ..       3     163 .. 0.99

  Alignments for each domain:
  == domain 1  score: 278.0 bits;  conditional E-value: 8.7e-88
                       TIGR01261   1 qkilfidrdGtlieePksdfqvdaleklklekkvipallklkeagyklvlvtnqdGlGtesfPkedfdkphalmlqifk 79 
                                     qk+lfidrdGtli+eP+sdfqvd+++kl++e++vip+llkl++agyklv++tnqdGlGt+sfP++dfd+ph+lm+qif+
  lcl|FitnessBrowser__Keio:16130   3 QKYLFIDRDGTLISEPPSDFQVDRFDKLAFEPGVIPELLKLQKAGYKLVMITNQDGLGTQSFPQADFDGPHNLMMQIFT 81 
                                     79***************************************************************************** PP

                       TIGR01261  80 seGivfddvlicphfledncacrkPkiklleeylkkekidkersyviGdretdlqlaenlgirglkykeeelnwkeiak 158
                                     s+G++fd+vlicph+++d+c+crkPk+kl+e+yl+++++d+++syviGdr+td+qlaen+gi+gl+y++e+lnw +i +
  lcl|FitnessBrowser__Keio:16130  82 SQGVQFDEVLICPHLPADECDCRKPKVKLVERYLAEQAMDRANSYVIGDRATDIQLAENMGITGLRYDRETLNWPMIGE 160
                                     ******************************************************************************9 PP

                       TIGR01261 159 el 160
                                     +l
  lcl|FitnessBrowser__Keio:16130 161 QL 162
                                     98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (161 nodes)
Target sequences:                          1  (355 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: 9.18
//
[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