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

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 200399 SO1221 purine nucleoside phosphorylase (NCBI ptt file)

Query= BRENDA::P0ABP8
         (239 letters)



>FitnessBrowser__MR1:200399
          Length = 236

 Score =  337 bits (865), Expect = 9e-98
 Identities = 162/234 (69%), Positives = 197/234 (84%)

Query: 1   MATPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISV 60
           MATPHINA  G FA+ VL PGDPLRAKYIAETFLE+  +V +VR MLGFTGTYKG++ISV
Sbjct: 1   MATPHINAVEGAFAETVLFPGDPLRAKYIAETFLENVEQVTDVRNMLGFTGTYKGKRISV 60

Query: 61  MGHGMGIPSCSIYTKELITDFGVKKIIRVGSCGAVLPHVKLRDVVIGMGACTDSKVNRIR 120
           MG GMGIPSCSIY  ELI D+GVK +IRVG+CGA+   VK+RDV+IGMGACTDS+VNR+R
Sbjct: 61  MGSGMGIPSCSIYATELIKDYGVKNLIRVGTCGAISTDVKVRDVIIGMGACTDSQVNRLR 120

Query: 121 FKDHDFAAIADFDMVRNAVDAAKALGIDARVGNLFSADLFYSPDGEMFDVMEKYGILGVE 180
           FK  DFAAIA+++++   +++AK  G   RVGN+FSADLFY+PD +MFDVMEK G+LGVE
Sbjct: 121 FKGQDFAAIANYELMNAVIESAKVKGTKIRVGNVFSADLFYTPDPQMFDVMEKMGVLGVE 180

Query: 181 MEAAGIYGVAAEFGAKALTICTVSDHIRTHEQTTAAERQTTFNDMIKIALESVL 234
           MEAAG+YGVA EFGA+AL + TVSDHIRT E+TT+ ERQTTFNDMI + L++ +
Sbjct: 181 MEAAGLYGVAHEFGARALCVVTVSDHIRTGEKTTSEERQTTFNDMIVMTLDAAI 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: 273
Number of extensions: 10
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 200399 SO1221 (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.10353.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   3.4e-115  369.4   0.9   3.7e-115  369.3   0.9    1.0  1  lcl|FitnessBrowser__MR1:200399  SO1221 purine nucleoside phospho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:200399  SO1221 purine nucleoside phosphorylase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  369.3   0.9  3.7e-115  3.7e-115       1     229 [.       5     233 ..       5     236 .] 0.99

  Alignments for each domain:
  == domain 1  score: 369.3 bits;  conditional E-value: 3.7e-115
                       TIGR00107   1 hinakkgdiadvvllpGdPlrakyiaekfledakevnevrgmlgftGkykgkkisvmGhGmGipsisiyskelikeyev 79 
                                     hina +g++a++vl+pGdPlrakyiae+fle++++v++vr+mlgftG+ykgk+isvmG GmGips+siy++elik+y+v
  lcl|FitnessBrowser__MR1:200399   5 HINAVEGAFAETVLFPGDPLRAKYIAETFLENVEQVTDVRNMLGFTGTYKGKRISVMGSGMGIPSCSIYATELIKDYGV 83 
                                     9****************************************************************************** PP

                       TIGR00107  80 kkiirvGsCGairkkvklkdviialkastdskvnrvrfvevdlaaiadfelvklakeaakkkgldvkvGnvfsadlfys 158
                                     k++irvG+CGai+++vk++dvii+++a+tds+vnr rf+ +d+aaia++el+++  e+ak kg +++vGnvfsadlfy+
  lcl|FitnessBrowser__MR1:200399  84 KNLIRVGTCGAISTDVKVRDVIIGMGACTDSQVNRLRFKGQDFAAIANYELMNAVIESAKVKGTKIRVGNVFSADLFYT 162
                                     ******************************************************************************* PP

                       TIGR00107 159 tdkevldllekygvlavemeaaalyavaaelgkkaltlltvsdhlvthealtaeerqktfkdmielalesv 229
                                     +d +++d++ek gvl+vemeaa+ly+va e+g++al+++tvsdh++t e++t+eerq+tf+dmi ++l+++
  lcl|FitnessBrowser__MR1:200399 163 PDPQMFDVMEKMGVLGVEMEAAGLYGVAHEFGARALCVVTVSDHIRTGEKTTSEERQTTFNDMIVMTLDAA 233
                                     ********************************************************************976 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 8.62
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources