Alignments for a candidate for deoD in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoD in Shewanella loihica PV-4

Align purine-nucleoside phosphorylase (EC 2.4.2.1) (characterized)
to candidate 5210369 Shew_2812 purine nucleoside phosphorylase (RefSeq)

Query= BRENDA::P0ABP8
         (239 letters)



>FitnessBrowser__PV4:5210369
          Length = 236

 Score =  333 bits (853), Expect = 2e-96
 Identities = 164/234 (70%), Positives = 193/234 (82%)

Query: 1   MATPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISV 60
           MATPHINA  G FAD VL PGDPLRAKYIAETFLE+  +V +VR MLGFTGTYKG +ISV
Sbjct: 1   MATPHINAVDGAFADTVLFPGDPLRAKYIAETFLENVEQVTDVRNMLGFTGTYKGVRISV 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  DFAAI D+ ++   V AA+  G   RVGN+FSADLFY+PD EMFDVMEK  +LGVE
Sbjct: 121 FKGQDFAAICDYSLLSAVVKAAEEKGTKYRVGNVFSADLFYTPDPEMFDVMEKMDVLGVE 180

Query: 181 MEAAGIYGVAAEFGAKALTICTVSDHIRTHEQTTAAERQTTFNDMIKIALESVL 234
           MEAAG+YGVA EFGAKAL + TVSDHIRT E+T++ ERQTTFN+MI++ LE+ +
Sbjct: 181 MEAAGLYGVAKEFGAKALCVVTVSDHIRTGEKTSSDERQTTFNEMIEMTLEAAI 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: 269
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: 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 5210369 Shew_2812 (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.15952.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   6.7e-114  365.2   0.6   7.4e-114  365.0   0.6    1.0  1  lcl|FitnessBrowser__PV4:5210369  Shew_2812 purine nucleoside phos


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5210369  Shew_2812 purine nucleoside phosphorylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  365.0   0.6  7.4e-114  7.4e-114       1     229 [.       5     233 ..       5     236 .] 0.99

  Alignments for each domain:
  == domain 1  score: 365.0 bits;  conditional E-value: 7.4e-114
                        TIGR00107   1 hinakkgdiadvvllpGdPlrakyiaekfledakevnevrgmlgftGkykgkkisvmGhGmGipsisiyskelikeye 78 
                                      hina  g++ad+vl+pGdPlrakyiae+fle++++v++vr+mlgftG+ykg +isvmG GmGips+siy++elik+y+
  lcl|FitnessBrowser__PV4:5210369   5 HINAVDGAFADTVLFPGDPLRAKYIAETFLENVEQVTDVRNMLGFTGTYKGVRISVMGSGMGIPSCSIYATELIKDYG 82 
                                      9***************************************************************************** PP

                        TIGR00107  79 vkkiirvGsCGairkkvklkdviialkastdskvnrvrfvevdlaaiadfelvklakeaakkkgldvkvGnvfsadlf 156
                                      vk++irvG+CGai+++vk++dvii+++a+tds+vnr rf+ +d+aai d++l+ + ++aa++kg + +vGnvfsadlf
  lcl|FitnessBrowser__PV4:5210369  83 VKNLIRVGTCGAISTDVKVRDVIIGMGACTDSQVNRLRFKGQDFAAICDYSLLSAVVKAAEEKGTKYRVGNVFSADLF 160
                                      ****************************************************************************** PP

                        TIGR00107 157 ystdkevldllekygvlavemeaaalyavaaelgkkaltlltvsdhlvthealtaeerqktfkdmielalesv 229
                                      y++d e++d++ek +vl+vemeaa+ly+va e+g+kal+++tvsdh++t e+++++erq+tf++mie++le++
  lcl|FitnessBrowser__PV4:5210369 161 YTPDPEMFDVMEKMDVLGVEMEAAGLYGVAKEFGAKALCVVTVSDHIRTGEKTSSDERQTTFNEMIEMTLEAA 233
                                      **********************************************************************986 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: 8.51
//
[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