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.31120.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: 00:00:00.04
# Mc/sec: 1.17
//
[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