GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdaB in Echinicola vietnamensis KMM 6221, DSM 17526

Align Probable L-serine dehydratase, beta chain; SDH; EC 4.3.1.17; L-serine deaminase; L-SD (uncharacterized)
to candidate Echvi_2833 Echvi_2833 L-serine dehydratase, iron-sulfur-dependent, beta subunit

Query= curated2:O34635
         (220 letters)



>FitnessBrowser__Cola:Echvi_2833
          Length = 225

 Score =  171 bits (433), Expect = 1e-47
 Identities = 91/217 (41%), Positives = 133/217 (61%), Gaps = 1/217 (0%)

Query: 5   SVFDIIGPVMIGPSSSHTAGAARIGRVARSLFGREPERIIVSFYGSFAETYKGHGTDVAI 64
           SVFD+IGPVMIGPSSSHTAG  RI R A  + G  P+  +++FY SFA TY+GHG+D AI
Sbjct: 6   SVFDMIGPVMIGPSSSHTAGVVRIARAAIKVLGGIPDDAVITFYNSFARTYEGHGSDKAI 65

Query: 65  IGGLLDFDTFDERIKTAIQIAEAKGIDIEFR-VEDAVPVHPNTAKITISDEKGELELTGI 123
           IGGL+D  T D RIK A ++AEA+G+   F+ V +A   HPNT K+ ++    ++E+ G 
Sbjct: 66  IGGLMDLKTDDARIKQAFELAEARGLTYIFKSVGNASVFHPNTIKLNLTKGDRKVEVIGE 125

Query: 124 SIGGGKIEITELNGFELRLSGNHPAILVVHNDKFGTIAGVANVLAKFSINVGHMEVARKD 183
           S+GGG I I  ++GF    S     +++  +D  G IA + ++LA+   N+  M V+RK 
Sbjct: 126 SLGGGLINIKSIDGFHAEFSAQEHTLIIKADDVSGAIAFITSILAQEQANIATMSVSRKG 185

Query: 184 IGQLALMTIEVDQNIDDHILDELSKLPNIIQVTKIAD 220
              +A   IE+D  ++   +  L  +  I ++  I D
Sbjct: 186 KRDMACHVIEMDSGLNAITIKYLESISWIHELIYIPD 222


Lambda     K      H
   0.319    0.140    0.390 

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: 144
Number of extensions: 5
Number of successful extensions: 2
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: 220
Length of database: 225
Length adjustment: 22
Effective length of query: 198
Effective length of database: 203
Effective search space:    40194
Effective search space used:    40194
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 (21.7 bits)
S2: 45 (21.9 bits)

Align candidate Echvi_2833 Echvi_2833 (L-serine dehydratase, iron-sulfur-dependent, beta subunit)
to HMM TIGR00719 (sdaAB: L-serine dehydratase, iron-sulfur-dependent, beta subunit (EC 4.3.1.17))

# 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/TIGR00719.hmm
# target sequence database:        /tmp/gapView.24169.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00719  [M=208]
Accession:   TIGR00719
Description: sda_beta: L-serine dehydratase, iron-sulfur-dependent, beta subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
    2.3e-63  199.7   3.7    2.8e-63  199.4   3.7    1.0  1  lcl|FitnessBrowser__Cola:Echvi_2833  Echvi_2833 L-serine dehydratase,


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2833  Echvi_2833 L-serine dehydratase, iron-sulfur-dependent, beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.4   3.7   2.8e-63   2.8e-63       3     201 ..       4     201 ..       1     207 [. 0.96

  Alignments for each domain:
  == domain 1  score: 199.4 bits;  conditional E-value: 2.8e-63
                            TIGR00719   3 drsvfeviGpvmvGpssshtaGaakiarvarslvsreyervivslyGsfaetykGhGtdvalvGGlldfetdde 76 
                                          + svf++iGpvm+GpssshtaG ++iar a  +++  ++  ++++y sfa+ty GhG+d+a++GGl+d++tdd 
  lcl|FitnessBrowser__Cola:Echvi_2833   4 KSSVFDMIGPVMIGPSSSHTAGVVRIARAAIKVLGGIPDDAVITFYNSFARTYEGHGSDKAIIGGLMDLKTDDA 77 
                                          569*********************************************************************** PP

                            TIGR00719  77 riktaielakakGldiifrvedlvdnvhpnsvkivisdekGeeeeliGisiGGGkikivelnGielelrGeysa 150
                                          rik a+ela+a+Gl +if+    +  +hpn++k+ +++ + +  e+iG s+GGG i+i  ++G++ e++ +  +
  lcl|FitnessBrowser__Cola:Echvi_2833  78 RIKQAFELAEARGLTYIFKSVGNASVFHPNTIKLNLTKGDRK-VEVIGESLGGGLINIKSIDGFHAEFSAQEHT 150
                                          ******************99888888********99987776.99***************************** PP

                            TIGR00719 151 illvynekrGviayvasllakseinveslevkkkdltqlvlltvevdknld 201
                                          ++++ ++  G+ia+++s+la+ + n+ ++ v +k   +++   +e+d  l+
  lcl|FitnessBrowser__Cola:Echvi_2833 151 LIIKADDVSGAIAFITSILAQEQANIATMSVSRKGKRDMACHVIEMDSGLN 201
                                          ***********************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (208 nodes)
Target sequences:                          1  (225 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: 9.91
//
[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