GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisF in Methylohalobius crimeensis 10Ki

Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate WP_022948100.1 H035_RS0106020 imidazole glycerol phosphate synthase subunit HisF

Query= BRENDA::Q5NMD6
         (255 letters)



>NCBI__GCF_000421465.1:WP_022948100.1
          Length = 252

 Score =  330 bits (845), Expect = 2e-95
 Identities = 159/251 (63%), Positives = 200/251 (79%)

Query: 1   MTLCTRIIPCLDVADGRVVKGVNFTDLMDAGDPVEQAKVYDAAGADELCFLDISASHEGR 60
           M L  RIIPCLDV  GRVVKGV F D+ DAGDPVE A+ YD  GADEL FLDI+ASHEGR
Sbjct: 1   MGLAKRIIPCLDVDRGRVVKGVQFVDIRDAGDPVEIARRYDEEGADELTFLDITASHEGR 60

Query: 61  GTMLDVVARTAEVCFMPLTVGGGVRQVEDARALLLAGADKVAVNSAAVARPELVAEIADR 120
            TM+ VV + A   F+PLTVGGG+R ++D R +L AGADKVA+N+AAV  PE V + A+R
Sbjct: 61  DTMVHVVEQVAGCVFIPLTVGGGIRTLDDIRRMLNAGADKVAINTAAVFHPEFVQQAAER 120

Query: 121 FGAQCVVAAIDARRNGDHWEVYTHGGRRPTGINALDHALNLTRLGAGEILLTSMDKDGTR 180
           FG+QC+V AIDA+R GDHWE++THGGR+PTG++A+D A  +  LGAGEILLTSMD+DGT+
Sbjct: 121 FGSQCIVVAIDAKRVGDHWEIFTHGGRKPTGLDAVDWAAKMEALGAGEILLTSMDRDGTK 180

Query: 181 DGYDLELTRLVADSVPVPVIASGGVGNLDHMVEGVTKGHASALLAASIFHFGQYSLAEAH 240
           +G+DL LTR V++ V +PVIASGGVGNL+H+ EG+ +G A A+LAASIFHFG+YS+ +A 
Sbjct: 181 EGFDLALTRAVSERVGIPVIASGGVGNLEHLAEGIVEGRADAVLAASIFHFGEYSIHQAK 240

Query: 241 EALAKAGLTVR 251
             L + G+ VR
Sbjct: 241 AYLTERGIEVR 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: 256
Number of extensions: 10
Number of successful extensions: 1
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: 252
Length adjustment: 24
Effective length of query: 231
Effective length of database: 228
Effective search space:    52668
Effective search space used:    52668
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 WP_022948100.1 H035_RS0106020 (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.29438.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     2e-122  393.3   1.6   2.3e-122  393.1   1.6    1.0  1  lcl|NCBI__GCF_000421465.1:WP_022948100.1  H035_RS0106020 imidazole glycero


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000421465.1:WP_022948100.1  H035_RS0106020 imidazole glycerol phosphate synthase subunit HisF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  393.1   1.6  2.3e-122  2.3e-122       1     254 []       2     251 ..       2     251 .. 0.99

  Alignments for each domain:
  == domain 1  score: 393.1 bits;  conditional E-value: 2.3e-122
                                 TIGR00735   1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevverv 69 
                                               +lakriipCLdv++grvvkGvqf ++rdaGdpve+a++ydeeGadel+flditas+e+r+tm++vve+v
  lcl|NCBI__GCF_000421465.1:WP_022948100.1   2 GLAKRIIPCLDVDRGRVVKGVQFVDIRDAGDPVEIARRYDEEGADELTFLDITASHEGRDTMVHVVEQV 70 
                                               59******************************************************************* PP

                                 TIGR00735  70 aekvfiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaene 138
                                               a  vfiPltvgGGi++++d++++l+aGadkv+intaav +pe+++++a+rfGsq+ivvaidakr+ +  
  lcl|NCBI__GCF_000421465.1:WP_022948100.1  71 AGCVFIPLTVGGGIRTLDDIRRMLNAGADKVAINTAAVFHPEFVQQAAERFGSQCIVVAIDAKRVGD-- 137
                                               ****************************************************************997.. PP

                                 TIGR00735 139 eakyevtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgG 207
                                                 ++e+ ++gGr+ t+ld+v+wa+++e+lGaGeilltsmd+dGtk+G+dl+l+++v+e+v iPviasgG
  lcl|NCBI__GCF_000421465.1:WP_022948100.1 138 --HWEIFTHGGRKPTGLDAVDWAAKMEALGAGEILLTSMDRDGTKEGFDLALTRAVSERVGIPVIASGG 204
                                               ..5****************************************************************** PP

                                 TIGR00735 208 aGkaehleeaflkgkadaaLaasvfhkreltieevkeylaergvkvr 254
                                               +G+ ehl+e++++g+ada+Laas+fh++e++i++ k+yl+erg++vr
  lcl|NCBI__GCF_000421465.1:WP_022948100.1 205 VGNLEHLAEGIVEGRADAVLAASIFHFGEYSIHQAKAYLTERGIEVR 251
                                               **********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (254 nodes)
Target sequences:                          1  (252 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: 9.62
//
[ok]

This GapMind analysis is from Apr 10 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