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 199289 SO0092 purine nucleoside phosphorylase (NCBI ptt file)

Query= BRENDA::P0ABP8
         (239 letters)



>FitnessBrowser__MR1:199289
          Length = 236

 Score =  286 bits (733), Expect = 2e-82
 Identities = 132/234 (56%), Positives = 178/234 (76%)

Query: 1   MATPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISV 60
           M+TPHINA  GDFA  ++M GDPLRAK IAET+LED +EV NVRG+LGFTG YK + IS+
Sbjct: 1   MSTPHINANPGDFAKTIIMSGDPLRAKLIAETYLEDVKEVTNVRGILGFTGKYKSKDISI 60

Query: 61  MGHGMGIPSCSIYTKELITDFGVKKIIRVGSCGAVLPHVKLRDVVIGMGACTDSKVNRIR 120
           MGHGMG PS SIY  EL+  +GVK  IRVGSCGA+  ++ L+D+++ MGA TDSK+NRIR
Sbjct: 61  MGHGMGAPSASIYFHELMATYGVKNFIRVGSCGAISDNIHLKDLIVAMGASTDSKINRIR 120

Query: 121 FKDHDFAAIADFDMVRNAVDAAKALGIDARVGNLFSADLFYSPDGEMFDVMEKYGILGVE 180
           F DHD AAIA++D+++  ++  K   ++ +VGN+FS+DLFY P+   + +M KYG+LGVE
Sbjct: 121 FLDHDLAAIANYDLLQACIEVLKTTTVNYKVGNVFSSDLFYRPNENDYTLMAKYGVLGVE 180

Query: 181 MEAAGIYGVAAEFGAKALTICTVSDHIRTHEQTTAAERQTTFNDMIKIALESVL 234
           ME   +Y +AAE   +AL +CTV+DHI  HE  TA ER+T  ++M+K+ALE+ +
Sbjct: 181 MEVNALYALAAEHQCRALALCTVTDHIVQHEHLTADERRTDLHEMVKVALETAI 234


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: 218
Number of extensions: 5
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: 236
Length adjustment: 23
Effective length of query: 216
Effective length of database: 213
Effective search space:    46008
Effective search space used:    46008
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 199289 SO0092 (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.6325.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.1e-103  330.8   1.5   2.4e-103  330.7   1.5    1.0  1  lcl|FitnessBrowser__MR1:199289  SO0092 purine nucleoside phospho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:199289  SO0092 purine nucleoside phosphorylase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  330.7   1.5  2.4e-103  2.4e-103       1     230 [.       5     234 ..       5     236 .] 0.99

  Alignments for each domain:
  == domain 1  score: 330.7 bits;  conditional E-value: 2.4e-103
                       TIGR00107   1 hinakkgdiadvvllpGdPlrakyiaekfledakevnevrgmlgftGkykgkkisvmGhGmGipsisiyskelikeyev 79 
                                     hina+ gd+a++++++GdPlrak iae++led+kev++vrg+lgftGkyk+k is+mGhGmG ps siy +el+ +y+v
  lcl|FitnessBrowser__MR1:199289   5 HINANPGDFAKTIIMSGDPLRAKLIAETYLEDVKEVTNVRGILGFTGKYKSKDISIMGHGMGAPSASIYFHELMATYGV 83 
                                     9****************************************************************************** PP

                       TIGR00107  80 kkiirvGsCGairkkvklkdviialkastdskvnrvrfvevdlaaiadfelvklakeaakkkgldvkvGnvfsadlfys 158
                                     k+ irvGsCGai+ +++lkd+i+a++astdsk+nr+rf ++dlaaia+++l+++  e  k+  ++ kvGnvfs+dlfy+
  lcl|FitnessBrowser__MR1:199289  84 KNFIRVGSCGAISDNIHLKDLIVAMGASTDSKINRIRFLDHDLAAIANYDLLQACIEVLKTTTVNYKVGNVFSSDLFYR 162
                                     ******************************************************************************* PP

                       TIGR00107 159 tdkevldllekygvlavemeaaalyavaaelgkkaltlltvsdhlvthealtaeerqktfkdmielalesvs 230
                                     ++++   l++kygvl+veme +alya+aae++ +al+l+tv+dh+v he+lta+er++ +++m+++ale++ 
  lcl|FitnessBrowser__MR1:199289 163 PNENDYTLMAKYGVLGVEMEVNALYALAAEHQCRALALCTVTDHIVQHEHLTADERRTDLHEMVKVALETAI 234
                                     ********************************************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (232 nodes)
Target sequences:                          1  (236 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.45
//
[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