GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisF in Phaeobacter inhibens BS107

Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate GFF908 PGA1_c09240 imidazole glycerol phosphate synthase subunit HisF

Query= BRENDA::Q5NMD6
         (255 letters)



>FitnessBrowser__Phaeo:GFF908
          Length = 253

 Score =  343 bits (880), Expect = 2e-99
 Identities = 171/250 (68%), Positives = 206/250 (82%), Gaps = 1/250 (0%)

Query: 3   LCTRIIPCLDVADGRVVKGVNFTDLMDAGDPVEQAKVYDAAGADELCFLDISASHEGRGT 62
           L TRIIPCLDVADGRVVKGVNF  L DAGDPVE AK YDAAGADE+CFLDI A+HE RGT
Sbjct: 2   LKTRIIPCLDVADGRVVKGVNFVGLRDAGDPVEAAKAYDAAGADEICFLDIHATHENRGT 61

Query: 63  MLDVVARTAEVCFMPLTVGGGVRQVEDARALLLAGADKVAVNSAAVARPELVAEIADRFG 122
           M D+V RTAE CF+PLTVGGGVR  ED RALLLAGADKV+ NSAAVA P+++ E AD+FG
Sbjct: 62  MFDMVRRTAEQCFVPLTVGGGVRTKEDVRALLLAGADKVSFNSAAVANPDVIREAADQFG 121

Query: 123 AQCVVAAIDARRNG-DHWEVYTHGGRRPTGINALDHALNLTRLGAGEILLTSMDKDGTRD 181
           +QC V AIDA+      WE++THGGRR TGI+A++ A  +   GAGEILLTSMD+DGT+ 
Sbjct: 122 SQCTVCAIDAKTVAPGKWEIFTHGGRRETGIDAVEFARLVVAKGAGEILLTSMDRDGTKS 181

Query: 182 GYDLELTRLVADSVPVPVIASGGVGNLDHMVEGVTKGHASALLAASIFHFGQYSLAEAHE 241
           G++L LTR ++D+V VPVIASGGVG LDH+VEGVT+G ASA+LAASIFHFG++++ EA +
Sbjct: 182 GFNLPLTRAISDAVDVPVIASGGVGTLDHLVEGVTEGGASAVLAASIFHFGEFTVQEAKQ 241

Query: 242 ALAKAGLTVR 251
            +A AG+ +R
Sbjct: 242 HMAAAGIPMR 251


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: 294
Number of extensions: 8
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: 255
Length of database: 253
Length adjustment: 24
Effective length of query: 231
Effective length of database: 229
Effective search space:    52899
Effective search space used:    52899
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 GFF908 PGA1_c09240 (imidazole glycerol phosphate synthase subunit HisF)
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.30920.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.6e-108  346.6   1.3     4e-108  346.5   1.3    1.0  1  lcl|FitnessBrowser__Phaeo:GFF908  PGA1_c09240 imidazole glycerol p


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF908  PGA1_c09240 imidazole glycerol phosphate synthase subunit HisF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  346.5   1.3    4e-108    4e-108       1     254 []       1     251 [.       1     251 [. 0.99

  Alignments for each domain:
  == domain 1  score: 346.5 bits;  conditional E-value: 4e-108
                         TIGR00735   1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevvervaekvfiPl 77 
                                       ml  riipCLdv dgrvvkGv+f  lrdaGdpve ak+yd+ Gade+ fldi a++e+r tm ++v+r+ae+ f+Pl
  lcl|FitnessBrowser__Phaeo:GFF908   1 MLKTRIIPCLDVADGRVVKGVNFVGLRDAGDPVEAAKAYDAAGADEICFLDIHATHENRGTMFDMVRRTAEQCFVPL 77 
                                       7999************************************************************************* PP

                         TIGR00735  78 tvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaeneeakyevtikgGrestd 154
                                       tvgGG+++ edv+ ll aGadkvs n+aav++p++i+e+ad+fGsq+ v aidak++a    +k+e+ ++gGr++t+
  lcl|FitnessBrowser__Phaeo:GFF908  78 TVGGGVRTKEDVRALLLAGADKVSFNSAAVANPDVIREAADQFGSQCTVCAIDAKTVAP---GKWEIFTHGGRRETG 151
                                       *******************************************************9997...69************* PP

                         TIGR00735 155 ldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgGaGkaehleeaflkgkadaaLaasv 231
                                       +d+ve+a+ v ++GaGeilltsmd+dGtksG++l l++++++av++PviasgG+G+ +hl e++++g a a+Laas+
  lcl|FitnessBrowser__Phaeo:GFF908 152 IDAVEFARLVVAKGAGEILLTSMDRDGTKSGFNLPLTRAISDAVDVPVIASGGVGTLDHLVEGVTEGGASAVLAASI 228
                                       ***************************************************************************** PP

                         TIGR00735 232 fhkreltieevkeylaergvkvr 254
                                       fh++e+t++e k+++a+ g+++r
  lcl|FitnessBrowser__Phaeo:GFF908 229 FHFGEFTVQEAKQHMAAAGIPMR 251
                                       ********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (254 nodes)
Target sequences:                          1  (253 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 7.10
//
[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:

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