GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisF in Pseudomonas fluorescens GW456-L13

Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate PfGW456L13_358 Imidazole glycerol phosphate synthase cyclase subunit (EC 4.1.3.-)

Query= BRENDA::Q5NMD6
         (255 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_358
          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 QDGMKNGFDLGVTRAISDALGIPVIASGGVGNLQHLADGIIEGHASAVLAASIFHFGEYT 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 PfGW456L13_358 (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.14028.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  377.5   0.7   1.6e-117  377.3   0.7    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_358  Imidazole glycerol phosphate syn


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_358  Imidazole glycerol phosphate synthase cyclase subunit (EC 4.1.
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  377.3   0.7  1.6e-117  1.6e-117       2     254 .]       3     256 .]       2     256 .] 0.98

  Alignments for each domain:
  == domain 1  score: 377.3 bits;  conditional E-value: 1.6e-117
                                              TIGR00735   2 lakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditasse 57 
                                                            lakriipCLdv++grvvkGv+f+n+rdaGdpve+a++yde+Gade++flditas +
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_358   3 LAKRIIPCLDVDNGRVVKGVKFENIRDAGDPVEIARRYDEQGADEITFLDITASVD 58 
                                                            9******************************************************* PP

                                              TIGR00735  58 kretmlevvervaekvfiPltvgGGiksiedvkkllraGadkvsintaavkapeli 113
                                                            +r+t l+ ver+a +vfiPltvgGG+++++d+++ll+aGadkvsintaav +pe++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_358  59 GRDTTLHTVERMASQVFIPLTVGGGVRTVQDIRNLLNAGADKVSINTAAVFNPEFV 114
                                                            ******************************************************** PP

                                              TIGR00735 114 keladrfGsqaivvaidakreae.neeakyevtikgGrestdldvvewakeveelG 168
                                                             e+a++fGsq+ivvaidak++    e   +e+ ++gGr+ t+ld+vewak++e lG
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_358 115 GEAAQHFGSQCIVVAIDAKKVSGpGETPRWEIFTHGGRKPTGLDAVEWAKKMEGLG 170
                                                            ******************9987525779**************************** PP

                                              TIGR00735 169 aGeilltsmdkdGtksGydlellkkvkeavkiPviasgGaGkaehleeaflkgkad 224
                                                            aGeilltsmd+dG+k+G+dl +++++++a+ iPviasgG+G+ +hl++++++g+a 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_358 171 AGEILLTSMDQDGMKNGFDLGVTRAISDALGIPVIASGGVGNLQHLADGIIEGHAS 226
                                                            ******************************************************** PP

                                              TIGR00735 225 aaLaasvfhkreltieevkeylaergvkvr 254
                                                            a+Laas+fh++e+t++e k+y+a+rg+ +r
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_358 227 AVLAASIFHFGEYTVQEAKAYMAHRGIVMR 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: 6.52
//
[ok]

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

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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:

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