GapMind for catabolism of small carbon sources

 

Aligments for a candidate for deoD in Phaeobacter inhibens BS107

Align purine-nucleoside phosphorylase (EC 2.4.2.1) (characterized)
to candidate GFF371 PGA1_c03820 purine nucleoside phosphorylase deoD-type

Query= BRENDA::O34925
         (233 letters)



>lcl|FitnessBrowser__Phaeo:GFF371 PGA1_c03820 purine nucleoside
           phosphorylase deoD-type
          Length = 234

 Score =  260 bits (664), Expect = 2e-74
 Identities = 124/231 (53%), Positives = 179/231 (77%), Gaps = 1/231 (0%)

Query: 1   MSVHIGAEKGQIADTVLLPGDPLRAKFIAETYLENVECYNEVRGMYGFTGTYKGKKISVQ 60
           M+VHIGA KG+IA+TVLLPGDP RAK+ AET+L++V   NEVRGM GFTGT+ G  +++Q
Sbjct: 1   MTVHIGAAKGEIAETVLLPGDPYRAKWAAETFLKDVRLVNEVRGMLGFTGTWNGHPVTIQ 60

Query: 61  GTGMGVPSISIYVNELIQSYDVQNLIRVGSCGAIRKDVKVRDVILAMTSSTDSQMNRVAF 120
           G+GMG+PS+SIYVNELI+ YD + LIR+GSCG ++  VK+RDVILAMT++T    +R  F
Sbjct: 61  GSGMGMPSLSIYVNELIRDYDAKTLIRIGSCGGMQDKVKIRDVILAMTATTTGSPSRGIF 120

Query: 121 GSVDFAPCADFELLKNAYDAAKDKGVPVTVGSVFTADQFYNDDSQI-EKLAKYGVLGVEM 179
             V+FAPCAD+ LL+ A  AA+   +   +G ++++D FY++   + E++ ++G+LGVEM
Sbjct: 121 KEVNFAPCADWSLLQAAVKAAETHELTPHIGGIYSSDVFYDERPDLNEQMVRHGILGVEM 180

Query: 180 ETTALYTLAAKHGRKALSILTVSDHVLTGEETTAEERQTTFHDMIEVALHS 230
           E   LYTLAA++G +AL++LTVSDH+ TGE   +++R+ +F DM+E+AL +
Sbjct: 181 EAAELYTLAARYGCRALAVLTVSDHLGTGEALPSDQRERSFGDMVEIALEA 231


Lambda     K      H
   0.317    0.133    0.370 

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: 189
Number of extensions: 7
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: 233
Length of database: 234
Length adjustment: 23
Effective length of query: 210
Effective length of database: 211
Effective search space:    44310
Effective search space used:    44310
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 46 (22.3 bits)

Align candidate GFF371 PGA1_c03820 (purine nucleoside phosphorylase deoD-type)
to HMM TIGR00107 (deoD: purine nucleoside phosphorylase (EC 2.4.2.1))

# 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.carbon/TIGR00107.hmm
# target sequence database:        /tmp/gapView.13678.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00107  [M=232]
Accession:   TIGR00107
Description: deoD: purine nucleoside phosphorylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    2.4e-93  297.9   0.0    2.7e-93  297.8   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF371  PGA1_c03820 purine nucleoside ph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF371  PGA1_c03820 purine nucleoside phosphorylase deoD-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  297.8   0.0   2.7e-93   2.7e-93       1     229 [.       4     232 ..       4     234 .] 0.99

  Alignments for each domain:
  == domain 1  score: 297.8 bits;  conditional E-value: 2.7e-93
                         TIGR00107   1 hinakkgdiadvvllpGdPlrakyiaekfledakevnevrgmlgftGkykgkkisvmGhGmGipsisiyskelikey 77 
                                       hi+a kg+ia++vllpGdP rak+ ae+fl+d+++vnevrgmlgftG++ g+ ++++G GmG+ps+siy++eli++y
  lcl|FitnessBrowser__Phaeo:GFF371   4 HIGAAKGEIAETVLLPGDPYRAKWAAETFLKDVRLVNEVRGMLGFTGTWNGHPVTIQGSGMGMPSLSIYVNELIRDY 80 
                                       9**************************************************************************** PP

                         TIGR00107  78 evkkiirvGsCGairkkvklkdviialkastdskvnrvrfvevdlaaiadfelvklakeaakkkgldvkvGnvfsad 154
                                       + k++ir+GsCG ++ kvk++dvi+a++a+t    +r  f+ev++a++ad +l+++a++aa++++l+ ++G ++s+d
  lcl|FitnessBrowser__Phaeo:GFF371  81 DAKTLIRIGSCGGMQDKVKIRDVILAMTATTTGSPSRGIFKEVNFAPCADWSLLQAAVKAAETHELTPHIGGIYSSD 157
                                       ***************************************************************************** PP

                         TIGR00107 155 lfystdkevldllekygvlavemeaaalyavaaelgkkaltlltvsdhlvthealtaeerqktfkdmielalesv 229
                                       +fy+++ +  + + ++g+l+vemeaa ly++aa++g +al++ltvsdhl t eal++++r ++f dm+e+ale++
  lcl|FitnessBrowser__Phaeo:GFF371 158 VFYDERPDLNEQMVRHGILGVEMEAAELYTLAARYGCRALAVLTVSDHLGTGEALPSDQRERSFGDMVEIALEAA 232
                                       ************************************************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (232 nodes)
Target sequences:                          1  (234 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: 5.85
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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