GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__MR1:201857
          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.11063.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 7.82
//
[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