GapMind for catabolism of small carbon sources

 

Aligments for a candidate for deoD in Shewanella oneidensis MR-1

Align purine-nucleoside phosphorylase (EC 2.4.2.1) (characterized)
to candidate 201857 SO2719 purine nucleoside phosphorylase (NCBI ptt file)

Query= BRENDA::P0ABP8
         (239 letters)



>lcl|FitnessBrowser__MR1:201857 SO2719 purine nucleoside
           phosphorylase (NCBI ptt file)
          Length = 234

 Score =  260 bits (665), Expect = 1e-74
 Identities = 128/232 (55%), Positives = 167/232 (71%)

Query: 3   TPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISVMG 62
           T HINA+  DFA+ V+MPGDPLRAKYIAET+L DA EV NVR MLG+TG Y+G++ISVMG
Sbjct: 2   TAHINAQPTDFAETVIMPGDPLRAKYIAETYLTDAVEVTNVRNMLGYTGYYQGQRISVMG 61

Query: 63  HGMGIPSCSIYTKELITDFGVKKIIRVGSCGAVLPHVKLRDVVIGMGACTDSKVNRIRFK 122
           HGMGI S  +Y  ELI  FGVK+IIR+GS GA   HV++RDV++   A TDS  N  R  
Sbjct: 62  HGMGISSMVLYGHELINFFGVKRIIRIGSLGATQQHVEMRDVILAQAAGTDSPTNAKRSS 121

Query: 123 DHDFAAIADFDMVRNAVDAAKALGIDARVGNLFSADLFYSPDGEMFDVMEKYGILGVEME 182
            +  A  A F ++  A   A   GI  +VGN+FS DL+Y PD +M   +E++G+LG++ME
Sbjct: 122 GYHMATSATFSLLHKAYTKANEKGISVKVGNVFSGDLYYDPDEDMIPALERFGVLGIDME 181

Query: 183 AAGIYGVAAEFGAKALTICTVSDHIRTHEQTTAAERQTTFNDMIKIALESVL 234
            AG+YG+A + G ++L I TVSDH  T E+TTA ERQ +FN+MI++ALE+ L
Sbjct: 182 VAGLYGLAHQQGIESLAILTVSDHCLTGEETTAQERQLSFNNMIELALETAL 233


Lambda     K      H
   0.322    0.138    0.401 

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: 191
Number of extensions: 8
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: 239
Length of database: 234
Length adjustment: 23
Effective length of query: 216
Effective length of database: 211
Effective search space:    45576
Effective search space used:    45576
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 (21.9 bits)
S2: 46 (22.3 bits)

Align candidate 201857 SO2719 (purine nucleoside phosphorylase (NCBI ptt file))
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.24002.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    1.4e-95  305.2   0.1    1.6e-95  305.0   0.1    1.0  1  lcl|FitnessBrowser__MR1:201857  SO2719 purine nucleoside phospho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:201857  SO2719 purine nucleoside phosphorylase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.0   0.1   1.6e-95   1.6e-95       1     229 [.       4     232 ..       4     234 .] 0.99

  Alignments for each domain:
  == domain 1  score: 305.0 bits;  conditional E-value: 1.6e-95
                       TIGR00107   1 hinakkgdiadvvllpGdPlrakyiaekfledakevnevrgmlgftGkykgkkisvmGhGmGipsisiyskelikeyev 79 
                                     hina+  d+a++v++pGdPlrakyiae++l da ev++vr+mlg+tG y+g++isvmGhGmGi+s+ +y +eli++++v
  lcl|FitnessBrowser__MR1:201857   4 HINAQPTDFAETVIMPGDPLRAKYIAETYLTDAVEVTNVRNMLGYTGYYQGQRISVMGHGMGISSMVLYGHELINFFGV 82 
                                     9****************************************************************************** PP

                       TIGR00107  80 kkiirvGsCGairkkvklkdviialkastdskvnrvrfvevdlaaiadfelvklakeaakkkgldvkvGnvfsadlfys 158
                                     k+iir+Gs Ga +++v+++dvi+a+ a tds +n  r     +a+ a+f+l+++a+  a++kg++vkvGnvfs dl+y+
  lcl|FitnessBrowser__MR1:201857  83 KRIIRIGSLGATQQHVEMRDVILAQAAGTDSPTNAKRSSGYHMATSATFSLLHKAYTKANEKGISVKVGNVFSGDLYYD 161
                                     ******************************************************************************* PP

                       TIGR00107 159 tdkevldllekygvlavemeaaalyavaaelgkkaltlltvsdhlvthealtaeerqktfkdmielalesv 229
                                     +d++++  le+ gvl+++me a+ly++a + g ++l++ltvsdh +t e++ta+erq +f++mielale++
  lcl|FitnessBrowser__MR1:201857 162 PDEDMIPALERFGVLGIDMEVAGLYGLAHQQGIESLAILTVSDHCLTGEETTAQERQLSFNNMIELALETA 232
                                     ********************************************************************986 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 6.25
//
[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