GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisF in Flavobacterium glycines Gm-149

Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate WP_066326071.1 BLR17_RS13990 imidazole glycerol phosphate synthase subunit HisF

Query= BRENDA::Q9X0C6
         (253 letters)



>NCBI__GCF_900100165.1:WP_066326071.1
          Length = 251

 Score =  295 bits (755), Expect = 6e-85
 Identities = 149/251 (59%), Positives = 192/251 (76%), Gaps = 1/251 (0%)

Query: 1   MLAKRIIACLDVKDGRVVKGTNFENLRDSGDPVELGKFYSEIGIDELVFLDITASVEKRK 60
           ML KRII CLD+K+GR VKG NF +LRD+GDPVEL K YS+ G DELVFLDI+A+ E+R+
Sbjct: 1   MLTKRIIPCLDIKNGRTVKGVNFVDLRDAGDPVELAKIYSDEGADELVFLDISATEERRR 60

Query: 61  TMLELVEKVAEQIDIPFTVGGGIHDFETASELILRGADKVSINTAAVENPSLITQIAQTF 120
           T+++LV KVA  I+IPFTVGGGI   E    L+  GADKVSIN++AV+NP LI  +AQ F
Sbjct: 61  TLVDLVRKVASTINIPFTVGGGISAVEDVEVLLQNGADKVSINSSAVKNPQLINDLAQKF 120

Query: 121 GSQAVVVAIDAKRVDGEFMVFTYSGKKNTGILLRDWVVEVEKRGAGEILLTSIDRDGTKS 180
           GSQ VVVAIDAK++DG+++V    GK  T I L DW  EVE+RGAGEIL TS+D DGTK+
Sbjct: 121 GSQCVVVAIDAKQIDGQWIVHLVGGKVPTEIRLFDWAQEVERRGAGEILFTSMDNDGTKN 180

Query: 181 GYDTEMIRFVRPLTTLPIIASGGAGKMEHFLEAFLAG-ADAALAASVFHFREIDVRELKE 239
           G+  E +  +  L  +PIIASGGAG ++HF+++F  G ADAALAASVFHF+EI+++ LK 
Sbjct: 181 GFANEALAKLSNLVNIPIIASGGAGTIQHFVDSFTKGKADAALAASVFHFKEIEIKTLKN 240

Query: 240 YLKKHGVNVRL 250
            L+ + + VR+
Sbjct: 241 ELRNNNIEVRI 251


Lambda     K      H
   0.320    0.138    0.384 

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: 216
Number of extensions: 3
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: 253
Length of database: 251
Length adjustment: 24
Effective length of query: 229
Effective length of database: 227
Effective search space:    51983
Effective search space used:    51983
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: 46 (22.3 bits)

Align candidate WP_066326071.1 BLR17_RS13990 (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.3554379.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-110  354.5   0.9   1.5e-110  354.4   0.9    1.0  1  NCBI__GCF_900100165.1:WP_066326071.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900100165.1:WP_066326071.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  354.4   0.9  1.5e-110  1.5e-110       1     254 []       1     250 [.       1     250 [. 0.99

  Alignments for each domain:
  == domain 1  score: 354.4 bits;  conditional E-value: 1.5e-110
                             TIGR00735   1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevvervaekv 73 
                                           ml+kriipCLd+k+gr vkGv+f +lrdaGdpvelak y++eGadelvfldi+a++e+r+t++++v++va ++
  NCBI__GCF_900100165.1:WP_066326071.1   1 MLTKRIIPCLDIKNGRTVKGVNFVDLRDAGDPVELAKIYSDEGADELVFLDISATEERRRTLVDLVRKVASTI 73 
                                           8************************************************************************ PP

                             TIGR00735  74 fiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaeneeakyevti 146
                                            iP+tvgGGi+ +edv+ ll+ Gadkvsin++avk+p+li++la++fGsq++vvaidak+      +++ v+ 
  NCBI__GCF_900100165.1:WP_066326071.1  74 NIPFTVGGGISAVEDVEVLLQNGADKVSINSSAVKNPQLINDLAQKFGSQCVVVAIDAKQID----GQWIVHL 142
                                           **********************************************************9765....68***** PP

                             TIGR00735 147 kgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgGaGkaehleeafl 219
                                            gG+  t++ +++wa+eve++GaGeil+tsmd+dGtk+G+  e l k+++ v+iP+iasgGaG+ +h+ ++f+
  NCBI__GCF_900100165.1:WP_066326071.1 143 VGGKVPTEIRLFDWAQEVERRGAGEILFTSMDNDGTKNGFANEALAKLSNLVNIPIIASGGAGTIQHFVDSFT 215
                                           ************************************************************************* PP

                             TIGR00735 220 kgkadaaLaasvfhkreltieevkeylaergvkvr 254
                                           kgkadaaLaasvfh++e++i+ +k+ l++++++vr
  NCBI__GCF_900100165.1:WP_066326071.1 216 KGKADAALAASVFHFKEIEIKTLKNELRNNNIEVR 250
                                           **********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (254 nodes)
Target sequences:                          1  (251 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 21.30
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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