GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoD in Dinoroseobacter shibae DFL-12

Align purine-nucleoside phosphorylase (EC 2.4.2.1) (characterized)
to candidate 3609474 Dshi_2858 purine nucleoside phosphorylase (RefSeq)

Query= BRENDA::O34925
         (233 letters)



>FitnessBrowser__Dino:3609474
          Length = 234

 Score =  254 bits (650), Expect = 8e-73
 Identities = 126/231 (54%), Positives = 174/231 (75%), Gaps = 1/231 (0%)

Query: 1   MSVHIGAEKGQIADTVLLPGDPLRAKFIAETYLENVECYNEVRGMYGFTGTYKGKKISVQ 60
           M++HIGA  G IA+TVL+PGDPLRAK+ AET+L++  C NEVRGM GFTGT+ G ++++ 
Sbjct: 1   MTIHIGAAPGDIAETVLMPGDPLRAKWAAETFLDDPVCVNEVRGMLGFTGTWCGHRVTIH 60

Query: 61  GTGMGVPSISIYVNELIQSYDVQNLIRVGSCGAIRKDVKVRDVILAMTSSTDSQMNRVAF 120
           G+GMG+PS+SIY NELI  Y  Q LIR+GS GA++  V +RDVILAMT S+ S  +   F
Sbjct: 61  GSGMGMPSLSIYANELITEYGAQTLIRIGSTGAMQNHVALRDVILAMTCSSISTPSSGIF 120

Query: 121 GSVDFAPCADFELLKNAYDAAKDKGVPVTVGSVFTADQFYNDDSQI-EKLAKYGVLGVEM 179
             ++FAPCAD+ LLK A  AA  KG    VG ++++D FY++   + E++ ++GVLGVEM
Sbjct: 121 CELNFAPCADWGLLKAAEAAAGAKGTKTHVGGIYSSDVFYDERPDLTEQMIRHGVLGVEM 180

Query: 180 ETTALYTLAAKHGRKALSILTVSDHVLTGEETTAEERQTTFHDMIEVALHS 230
           E   LYTLAA+HGR+AL++LTVSDH+LT +   + ERQ++F DM+E+AL +
Sbjct: 181 EAAELYTLAARHGRRALAVLTVSDHLLTHDALPSAERQSSFGDMVEIALEA 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: 180
Number of extensions: 3
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 3609474 Dshi_2858 (purine nucleoside phosphorylase (RefSeq))
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.25049.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
      6e-93  296.6   0.0    6.7e-93  296.5   0.0    1.0  1  lcl|FitnessBrowser__Dino:3609474  Dshi_2858 purine nucleoside phos


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3609474  Dshi_2858 purine nucleoside phosphorylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  296.5   0.0   6.7e-93   6.7e-93       1     229 [.       4     232 ..       4     234 .] 0.99

  Alignments for each domain:
  == domain 1  score: 296.5 bits;  conditional E-value: 6.7e-93
                         TIGR00107   1 hinakkgdiadvvllpGdPlrakyiaekfledakevnevrgmlgftGkykgkkisvmGhGmGipsisiyskelikey 77 
                                       hi+a  gdia++vl+pGdPlrak+ ae+fl+d+ +vnevrgmlgftG++ g+++++ G GmG+ps+siy++eli+ey
  lcl|FitnessBrowser__Dino:3609474   4 HIGAAPGDIAETVLMPGDPLRAKWAAETFLDDPVCVNEVRGMLGFTGTWCGHRVTIHGSGMGMPSLSIYANELITEY 80 
                                       9**************************************************************************** PP

                         TIGR00107  78 evkkiirvGsCGairkkvklkdviialkastdskvnrvrfvevdlaaiadfelvklakeaakkkgldvkvGnvfsad 154
                                       + +++ir+Gs Ga++++v l+dvi+a+++s+ s  +   f e ++a++ad  l+k+a  aa +kg + +vG ++s+d
  lcl|FitnessBrowser__Dino:3609474  81 GAQTLIRIGSTGAMQNHVALRDVILAMTCSSISTPSSGIFCELNFAPCADWGLLKAAEAAAGAKGTKTHVGGIYSSD 157
                                       ***************************************************************************** PP

                         TIGR00107 155 lfystdkevldllekygvlavemeaaalyavaaelgkkaltlltvsdhlvthealtaeerqktfkdmielalesv 229
                                       +fy+++ +  + + ++gvl+vemeaa ly++aa++g++al++ltvsdhl+th+al+++erq++f dm+e+ale++
  lcl|FitnessBrowser__Dino:3609474 158 VFYDERPDLTEQMIRHGVLGVEMEAAELYTLAARHGRRALAVLTVSDHLLTHDALPSAERQSSFGDMVEIALEAA 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 8.10
//
[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 (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