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

GapMind for Amino acid biosynthesis

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

Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate Pf1N1B4_1623 Imidazole glycerol phosphate synthase cyclase subunit (EC 4.1.3.-)

Query= BRENDA::Q5NMD6
         (255 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1623
          Length = 256

 Score =  302 bits (773), Expect = 5e-87
 Identities = 149/256 (58%), Positives = 194/256 (75%), Gaps = 5/256 (1%)

Query: 1   MTLCTRIIPCLDVADGRVVKGVNFTDLMDAGDPVEQAKVYDAAGADELCFLDISASHEGR 60
           M L  RIIPCLDV +GRVVKGV F ++ DAGDPVE A+ YD  GADE+ FLDI+AS +GR
Sbjct: 1   MALAKRIIPCLDVDNGRVVKGVKFENIRDAGDPVEIARRYDEQGADEITFLDITASVDGR 60

Query: 61  GTMLDVVARTAEVCFMPLTVGGGVRQVEDARALLLAGADKVAVNSAAVARPELVAEIADR 120
            T L  V R A   F+PLTVGGGVR V+D R LL AGADKV++N+AAV  PE V E A  
Sbjct: 61  DTTLHTVERMASQVFIPLTVGGGVRTVQDIRNLLNAGADKVSINTAAVFNPEFVGEAAQH 120

Query: 121 FGAQCVVAAIDARR-----NGDHWEVYTHGGRRPTGINALDHALNLTRLGAGEILLTSMD 175
           FG+QC+V AIDA++         WE++THGGR+PTG++A++ A  +  LGAGEILLTSMD
Sbjct: 121 FGSQCIVVAIDAKKVSGPGETPRWEIFTHGGRKPTGLDAVEWAKKMEGLGAGEILLTSMD 180

Query: 176 KDGTRDGYDLELTRLVADSVPVPVIASGGVGNLDHMVEGVTKGHASALLAASIFHFGQYS 235
           +DG ++G+DL +TR ++D++ +PVIASGGVGNL H+ +G+ +GHASA+LAASIFHFG+Y+
Sbjct: 181 QDGMKNGFDLGVTRAISDALGIPVIASGGVGNLQHLADGILEGHASAVLAASIFHFGEYT 240

Query: 236 LAEAHEALAKAGLTVR 251
           + EA   +A  G+ +R
Sbjct: 241 VQEAKAYMAHRGIVMR 256


Lambda     K      H
   0.320    0.136    0.400 

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: 239
Number of extensions: 9
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: 255
Length of database: 256
Length adjustment: 24
Effective length of query: 231
Effective length of database: 232
Effective search space:    53592
Effective search space used:    53592
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 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.16185.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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 6.82
//
[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