Alignments for a candidate for deoC in Vagococcus penaei CD276

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoC in Vagococcus penaei CD276

Align Deoxyribose-phosphate aldolase; DERA; 2-deoxy-D-ribose 5-phosphate aldolase; Phosphodeoxyriboaldolase; Deoxyriboaldolase; EC 4.1.2.4 (characterized)
to candidate WP_077276702.1 BW732_RS10580 deoxyribose-phosphate aldolase

Query= SwissProt::P39121
         (223 letters)



>NCBI__GCF_001998885.1:WP_077276702.1
          Length = 217

 Score =  260 bits (665), Expect = 1e-74
 Identities = 137/211 (64%), Positives = 160/211 (75%)

Query: 3   LANIIDHTALKPHTQKADILKLIEEAKTYKFASVCVNPTWVELAAKELKGTGVDVCTVIG 62
           LA  IDHT L P T +++I  L +EAK   FASVCVNP WVEL  + L+ T V+VCTV+G
Sbjct: 7   LAKFIDHTTLLPGTTRSEIELLCKEAKKLGFASVCVNPYWVELCHELLQDTDVNVCTVVG 66

Query: 63  FPLGANTTETKAFETKDAISKGATEVDMVINIAALKDKEDDVVEADIRGVVEAVAGKALV 122
           FPLGANTTETK +E KDA+  GA E+DMVINI  LK   DD V+ADI  VV+A   KALV
Sbjct: 67  FPLGANTTETKVYEAKDAMKHGAVEIDMVINIGELKAGNDDAVKADIAAVVKACKKKALV 126

Query: 123 KVIIETCLLTDEEKERACRLAVSAGADFVKTSTGFSTGGATKEDIALMRKTVGPDIGVKA 182
           KVIIETCLLTD+EK RAC+LAV AGA+FVKTSTGFSTGGAT ED+ LM+ TV     VKA
Sbjct: 127 KVIIETCLLTDDEKVRACQLAVDAGAEFVKTSTGFSTGGATPEDVKLMKDTVKDLAQVKA 186

Query: 183 SGGVRTKEDVDTMVEAGASRIGASAGVSIVK 213
           SGGVR+KED   M+E GA+R+G SAG  IV+
Sbjct: 187 SGGVRSKEDAMKMLEMGAARLGTSAGSKIVR 217


Lambda     K      H
   0.312    0.130    0.356 

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: 212
Number of extensions: 4
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: 223
Length of database: 217
Length adjustment: 22
Effective length of query: 201
Effective length of database: 195
Effective search space:    39195
Effective search space used:    39195
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 45 (21.9 bits)

Align candidate WP_077276702.1 BW732_RS10580 (deoxyribose-phosphate aldolase)
to HMM TIGR00126 (deoC: deoxyribose-phosphate aldolase (EC 4.1.2.4))

# 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/TIGR00126.hmm
# target sequence database:        /tmp/gapView.2622737.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00126  [M=211]
Accession:   TIGR00126
Description: deoC: deoxyribose-phosphate aldolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.1e-93  298.5   7.7    1.3e-93  298.3   7.7    1.0  1  NCBI__GCF_001998885.1:WP_077276702.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001998885.1:WP_077276702.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.3   7.7   1.3e-93   1.3e-93       2     209 ..       7     215 ..       6     217 .] 0.99

  Alignments for each domain:
  == domain 1  score: 298.3 bits;  conditional E-value: 1.3e-93
                             TIGR00126   2 lakliDhtalkadtteedietlcaeAkkykfaavcvnpsyvslAkelLkgteveictvvgFPlGasttevkll 74 
                                           lak+iDht+l + tt+++ie lc+eAkk +fa+vcvnp +v+l +elL++t+v++ctvvgFPlGa+tte+k++
  NCBI__GCF_001998885.1:WP_077276702.1   7 LAKFIDHTTLLPGTTRSEIELLCKEAKKLGFASVCVNPYWVELCHELLQDTDVNVCTVVGFPLGANTTETKVY 79 
                                           89*********************************************************************** PP

                             TIGR00126  75 EakeaieeGAdEvDvviniaalkdkneevviedikavveaca.kvllKvilEtalLtdeekkkAseisieaga 146
                                           Eak+a+++GA E+D+vini++lk++n+++v++di+avv+ac  k+l+Kvi+Et+lLtd+ek++A++++++aga
  NCBI__GCF_001998885.1:WP_077276702.1  80 EAKDAMKHGAVEIDMVINIGELKAGNDDAVKADIAAVVKACKkKALVKVIIETCLLTDDEKVRACQLAVDAGA 152
                                           *****************************************9999**************************** PP

                             TIGR00126 147 dfvKtstgfsakgAtvedvrlmkkvvgdevgvKasGGvrtaedalalieagaerigasaavai 209
                                           +fvKtstgfs++gAt+edv+lmk++v+d  +vKasGGvr +eda++++e+ga r+g+sa+ +i
  NCBI__GCF_001998885.1:WP_077276702.1 153 EFVKTSTGFSTGGATPEDVKLMKDTVKDLAQVKASGGVRSKEDAMKMLEMGAARLGTSAGSKI 215
                                           ***********************************************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (211 nodes)
Target sequences:                          1  (217 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: 9.70
//
[ok]

This GapMind analysis is from Sep 24 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 2024 update 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