GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisF in Escherichia coli BW25113

Align IGP synthase cyclase subunit; EC 4.1.3.- (characterized)
to candidate 16133 b2025 imidazole glycerol phosphate synthase subunit HisF (NCBI)

Query= CharProtDB::CH_024847
         (258 letters)



>lcl|FitnessBrowser__Keio:16133 b2025 imidazole glycerol phosphate
           synthase subunit HisF (NCBI)
          Length = 258

 Score =  517 bits (1331), Expect = e-151
 Identities = 258/258 (100%), Positives = 258/258 (100%)

Query: 1   MLAKRIIPCLDVRDGQVVKGVQFRNHEIIGDIVPLAKRYAEEGADELVFYDITASSDGRV 60
           MLAKRIIPCLDVRDGQVVKGVQFRNHEIIGDIVPLAKRYAEEGADELVFYDITASSDGRV
Sbjct: 1   MLAKRIIPCLDVRDGQVVKGVQFRNHEIIGDIVPLAKRYAEEGADELVFYDITASSDGRV 60

Query: 61  VDKSWVSRVAEVIDIPFCVAGGIKSLEDAAKILSFGADKISINSPALADPTLITRLADRF 120
           VDKSWVSRVAEVIDIPFCVAGGIKSLEDAAKILSFGADKISINSPALADPTLITRLADRF
Sbjct: 61  VDKSWVSRVAEVIDIPFCVAGGIKSLEDAAKILSFGADKISINSPALADPTLITRLADRF 120

Query: 121 GVQCIVVGIDTWYDAETGKYHVNQYTGDESRTRVTQWETLDWVQEVQKRGAGEIVLNMMN 180
           GVQCIVVGIDTWYDAETGKYHVNQYTGDESRTRVTQWETLDWVQEVQKRGAGEIVLNMMN
Sbjct: 121 GVQCIVVGIDTWYDAETGKYHVNQYTGDESRTRVTQWETLDWVQEVQKRGAGEIVLNMMN 180

Query: 181 QDGVRNGYDLEQLKKVREVCHVPLIASGGAGTMEHFLEAFRDADVDGALAASVFHKQIIN 240
           QDGVRNGYDLEQLKKVREVCHVPLIASGGAGTMEHFLEAFRDADVDGALAASVFHKQIIN
Sbjct: 181 QDGVRNGYDLEQLKKVREVCHVPLIASGGAGTMEHFLEAFRDADVDGALAASVFHKQIIN 240

Query: 241 IGELKAYLATQGVEIRIC 258
           IGELKAYLATQGVEIRIC
Sbjct: 241 IGELKAYLATQGVEIRIC 258


Lambda     K      H
   0.321    0.138    0.409 

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: 414
Number of extensions: 11
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: 258
Length of database: 258
Length adjustment: 24
Effective length of query: 234
Effective length of database: 234
Effective search space:    54756
Effective search space used:    54756
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 (21.8 bits)
S2: 47 (22.7 bits)

Align candidate 16133 b2025 (imidazole glycerol phosphate synthase subunit HisF (NCBI))
to HMM TIGR00735 (hisF: imidazoleglycerol phosphate synthase, cyclase subunit)

# 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/TIGR00735.hmm
# target sequence database:        /tmp/gapView.7333.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00735  [M=254]
Accession:   TIGR00735
Description: hisF: imidazoleglycerol phosphate synthase, cyclase subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.6e-122  392.9   1.0   2.9e-122  392.8   1.0    1.0  1  lcl|FitnessBrowser__Keio:16133  b2025 imidazole glycerol phospha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:16133  b2025 imidazole glycerol phosphate synthase subunit HisF (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  392.8   1.0  2.9e-122  2.9e-122       1     254 []       1     256 [.       1     256 [. 0.99

  Alignments for each domain:
  == domain 1  score: 392.8 bits;  conditional E-value: 2.9e-122
                       TIGR00735   1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevvervaekvfiPltv 79 
                                     mlakriipCLdv+dg+vvkGvqf+n++ +Gd+v+lak+y+eeGadelvf+ditass++r +++++v+rvae ++iP++v
  lcl|FitnessBrowser__Keio:16133   1 MLAKRIIPCLDVRDGQVVKGVQFRNHEIIGDIVPLAKRYAEEGADELVFYDITASSDGRVVDKSWVSRVAEVIDIPFCV 79 
                                     8****************************************************************************** PP

                       TIGR00735  80 gGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaeneeakyevtikgGres....td 154
                                     +GGiks+ed++k+l++Gadk+sin++a+++p+li++ladrfG+q+ivv+id++++ae+  +ky+v++++G+es    t+
  lcl|FitnessBrowser__Keio:16133  80 AGGIKSLEDAAKILSFGADKISINSPALADPTLITRLADRFGVQCIVVGIDTWYDAET--GKYHVNQYTGDESrtrvTQ 156
                                     ******************************************************9987..9**********9988899* PP

                       TIGR00735 155 ldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgGaGkaehleeaflkgkadaaLaasvfh 233
                                     +++++w++ev+++GaGei+l++m++dG+++Gydle+lkkv+e++++P+iasgGaG++eh+ eaf ++++d+aLaasvfh
  lcl|FitnessBrowser__Keio:16133 157 WETLDWVQEVQKRGAGEIVLNMMNQDGVRNGYDLEQLKKVREVCHVPLIASGGAGTMEHFLEAFRDADVDGALAASVFH 235
                                     ******************************************************************************* PP

                       TIGR00735 234 kreltieevkeylaergvkvr 254
                                     k++++i+e+k+yla++gv++r
  lcl|FitnessBrowser__Keio:16133 236 KQIINIGELKAYLATQGVEIR 256
                                     ********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (254 nodes)
Target sequences:                          1  (258 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: 00:00:00.01
# Mc/sec: 5.85
//
[ok]

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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