GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisF in Pseudomonas fluorescens FW300-N1B4

Align Imidazole glycerol phosphate synthase subunit HisF; IGP synthase cyclase subunit; IGP synthase subunit HisF; ImGP synthase subunit HisF; IGPS subunit HisF; EC 4.3.2.10 (characterized)
to candidate Pf1N1B4_1623 Imidazole glycerol phosphate synthase cyclase subunit (EC 4.1.3.-)

Query= SwissProt::Q7SIB9
         (252 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1623 Imidazole glycerol
           phosphate synthase cyclase subunit (EC 4.1.3.-)
          Length = 256

 Score =  290 bits (741), Expect = 3e-83
 Identities = 150/256 (58%), Positives = 190/256 (74%), Gaps = 6/256 (2%)

Query: 1   MSLAKRIVPCLDVHAGRVVKGVNFVNLRDAGDPVEAARAYDEAGADELVFLDISATHEER 60
           M+LAKRI+PCLDV  GRVVKGV F N+RDAGDPVE AR YDE GADE+ FLDI+A+ + R
Sbjct: 1   MALAKRIIPCLDVDNGRVVKGVKFENIRDAGDPVEIARRYDEQGADEITFLDITASVDGR 60

Query: 61  AILLDVVARVAERVFIPLTVGGGVRSLEDARKLLLSGADKVSVNSAAVRRPELIRELADH 120
              L  V R+A +VFIPLTVGGGVR+++D R LL +GADKVS+N+AAV  PE + E A H
Sbjct: 61  DTTLHTVERMASQVFIPLTVGGGVRTVQDIRNLLNAGADKVSINTAAVFNPEFVGEAAQH 120

Query: 121 FGAQAVVLAIDAR---WRGDFP--EVHVAGGRVPTGLHAVEWAVKGVELGAGEILLTSMD 175
           FG+Q +V+AIDA+     G+ P  E+   GGR PTGL AVEWA K   LGAGEILLTSMD
Sbjct: 121 FGSQCIVVAIDAKKVSGPGETPRWEIFTHGGRKPTGLDAVEWAKKMEGLGAGEILLTSMD 180

Query: 176 RDGTKEGYDLRLTRMVAEAVGVPVIASGGAGRMEHFLEAFQAG-AEAALAASVFHFGEIP 234
           +DG K G+DL +TR +++A+G+PVIASGG G ++H  +    G A A LAAS+FHFGE  
Sbjct: 181 QDGMKNGFDLGVTRAISDALGIPVIASGGVGNLQHLADGILEGHASAVLAASIFHFGEYT 240

Query: 235 IPKLKRYLAEKGVHVR 250
           + + K Y+A +G+ +R
Sbjct: 241 VQEAKAYMAHRGIVMR 256


Lambda     K      H
   0.321    0.138    0.398 

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: 244
Number of extensions: 14
Number of successful extensions: 5
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: 252
Length of database: 256
Length adjustment: 24
Effective length of query: 228
Effective length of database: 232
Effective search space:    52896
Effective search space used:    52896
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: 47 (22.7 bits)

Align candidate Pf1N1B4_1623 (Imidazole glycerol phosphate synthase cyclase subunit (EC 4.1.3.-))
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.5449.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.4e-117  377.4   0.6   1.6e-117  377.2   0.6    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1623  Imidazole glycerol phosphate syn


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1623  Imidazole glycerol phosphate synthase cyclase subunit (EC 4.1.3.-)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  377.2   0.6  1.6e-117  1.6e-117       2     254 .]       3     256 .]       2     256 .] 0.98

  Alignments for each domain:
  == domain 1  score: 377.2 bits;  conditional E-value: 1.6e-117
                                      TIGR00735   2 lakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlev 65 
                                                    lakriipCLdv++grvvkGv+f+n+rdaGdpve+a++yde+Gade++flditas ++r+t l+ 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1623   3 LAKRIIPCLDVDNGRVVKGVKFENIRDAGDPVEIARRYDEQGADEITFLDITASVDGRDTTLHT 66 
                                                    9*************************************************************** PP

                                      TIGR00735  66 vervaekvfiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvai 129
                                                    ver+a +vfiPltvgGG+++++d+++ll+aGadkvsintaav +pe++ e+a++fGsq+ivvai
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1623  67 VERMASQVFIPLTVGGGVRTVQDIRNLLNAGADKVSINTAAVFNPEFVGEAAQHFGSQCIVVAI 130
                                                    **************************************************************** PP

                                      TIGR00735 130 dakreae.neeakyevtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellk 192
                                                    dak++    e   +e+ ++gGr+ t+ld+vewak++e lGaGeilltsmd+dG+k+G+dl +++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1623 131 DAKKVSGpGETPRWEIFTHGGRKPTGLDAVEWAKKMEGLGAGEILLTSMDQDGMKNGFDLGVTR 194
                                                    **9987525779**************************************************** PP

                                      TIGR00735 193 kvkeavkiPviasgGaGkaehleeaflkgkadaaLaasvfhkreltieevkeylaergvkvr 254
                                                    ++++a+ iPviasgG+G+ +hl++++l+g+a a+Laas+fh++e+t++e k+y+a+rg+ +r
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1623 195 AISDALGIPVIASGGVGNLQHLADGILEGHASAVLAASIFHFGEYTVQEAKAYMAHRGIVMR 256
                                                    ***********************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (254 nodes)
Target sequences:                          1  (256 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 6.97
//
[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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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