GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Dinoroseobacter shibae DFL-12

Align acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized)
to candidate 3609683 Dshi_3066 acetyl-CoA acetyltransferase (RefSeq)

Query= reanno::Phaeo:GFF329
         (391 letters)



>FitnessBrowser__Dino:3609683
          Length = 391

 Score =  714 bits (1842), Expect = 0.0
 Identities = 355/391 (90%), Positives = 372/391 (95%)

Query: 1   MTNVVIASAARTAVGSFGGAFAKTPAHDLGAAVLQAVVERAGIDKSEVSETILGQVLTAA 60
           MTNVVIASAARTAVGSFGG+FA TPAHDLG+AVL+A+V RAGI+K EVSETILGQVLT  
Sbjct: 1   MTNVVIASAARTAVGSFGGSFANTPAHDLGSAVLEALVARAGIEKGEVSETILGQVLTGG 60

Query: 61  QGQNPARQAHINAGLPQESAAWSLNQVCGSGLRAVALAAQHIQLGDAAIVCAGGQENMTL 120
           QGQNPARQAHINAGLPQESAAW LNQVCGSGLRAVAL AQHIQLGDA IVCAGGQENMTL
Sbjct: 61  QGQNPARQAHINAGLPQESAAWGLNQVCGSGLRAVALGAQHIQLGDAEIVCAGGQENMTL 120

Query: 121 SPHAANLRAGHKMGDMSYIDTMIRDGLWDAFNGYHMGQTAENVAEKWQISREMQDEFAVA 180
           SPH ANLRAG KMGDM +ID+MIRDGLWDAFNGYHMGQTAENVAEKWQISREMQDEFAVA
Sbjct: 121 SPHVANLRAGQKMGDMKFIDSMIRDGLWDAFNGYHMGQTAENVAEKWQISREMQDEFAVA 180

Query: 181 SQNKAEAAQKAGKFADEIAAFTVKTRKGDIIVDQDEYIRHGATIEAMQKLRPAFAKDGSV 240
           SQNKAEAAQKAGKF DE+ AFT+KTRKGDI+VD+DEYIRHGAT+EAMQKLRPAF KDGSV
Sbjct: 181 SQNKAEAAQKAGKFDDEVVAFTIKTRKGDIVVDKDEYIRHGATMEAMQKLRPAFTKDGSV 240

Query: 241 TAANASGLNDGAAATLLMSADDAEKRGIEPLARIASYATAGLDPSIMGVGPIYASRKALE 300
           TAANASGLNDGAA  LLMSA++AEKRGI P+ARIASYATAGLDPSIMGVGPIYASRKALE
Sbjct: 241 TAANASGLNDGAAGVLLMSAENAEKRGITPMARIASYATAGLDPSIMGVGPIYASRKALE 300

Query: 301 KAGWSVDDLDLVEANEAFAAQACAVNKDMGWDPAIVNVNGGAIAIGHPIGASGCRVLNTL 360
           KAGW VDDLDLVEANEAFAAQACAVNKDMGWDPAIVNVNGGAIAIGHPIGASG RVLNTL
Sbjct: 301 KAGWKVDDLDLVEANEAFAAQACAVNKDMGWDPAIVNVNGGAIAIGHPIGASGARVLNTL 360

Query: 361 LFEMKRRDAKKGLATLCIGGGMGVAMCVERP 391
           LFEM+RRDAKKGLATLCIGGGMGVA+CVERP
Sbjct: 361 LFEMQRRDAKKGLATLCIGGGMGVALCVERP 391


Lambda     K      H
   0.316    0.130    0.376 

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: 620
Number of extensions: 12
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: 391
Length of database: 391
Length adjustment: 31
Effective length of query: 360
Effective length of database: 360
Effective search space:   129600
Effective search space used:   129600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate 3609683 Dshi_3066 (acetyl-CoA acetyltransferase (RefSeq))
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

# 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/TIGR01930.hmm
# target sequence database:        /tmp/gapView.21218.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01930  [M=385]
Accession:   TIGR01930
Description: AcCoA-C-Actrans: acetyl-CoA C-acyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.2e-141  458.0  10.3   1.4e-141  457.8  10.3    1.0  1  lcl|FitnessBrowser__Dino:3609683  Dshi_3066 acetyl-CoA acetyltrans


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3609683  Dshi_3066 acetyl-CoA acetyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  457.8  10.3  1.4e-141  1.4e-141       1     385 []       6     389 ..       6     389 .. 0.98

  Alignments for each domain:
  == domain 1  score: 457.8 bits;  conditional E-value: 1.4e-141
                         TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpesvpal 77 
                                       i +a+Rt++g++ggs+++++a+dL++av+++l++rag+++ ++ e ilG+vl+ g+++n+aR+a ++aglp++ +a+
  lcl|FitnessBrowser__Dino:3609683   6 IASAARTAVGSFGGSFANTPAHDLGSAVLEALVARAGIEKGEVSETILGQVLTGGQGQNPARQAHINAGLPQESAAW 82 
                                       789************************************************************************** PP

                         TIGR01930  78 tvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl...vktklsm 151
                                        +n+vC+Sgl+Aval+aq+i+ G+a++v+aGG E+m+ +p++ +    r++ k+g++k  d++++d+   + ++++m
  lcl|FitnessBrowser__Dino:3609683  83 GLNQVCGSGLRAVALGAQHIQLGDAEIVCAGGQENMTLSPHVANL---RAGQKMGDMKFIDSMIRDGlwdAFNGYHM 156
                                       ****************************************98776...58999999**************99***** PP

                         TIGR01930 152 getAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpnttlekLakLkpa 226
                                       g+tAen+a+k++isRe+qDe+a++S++ka++A+++gkf+de+v +++k++  + vv+kDe ir + t+e+++kL+pa
  lcl|FitnessBrowser__Dino:3609683 157 GQTAENVAEKWQISREMQDEFAVASQNKAEAAQKAGKFDDEVVAFTIKTRkgDIVVDKDEYIRHGATMEAMQKLRPA 233
                                       ************************************************999999*********************** PP

                         TIGR01930 227 fkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisd 303
                                       f++ +gs vtA+N+s+lnDGAa +llms e a++ g+tp+ari s+a+ag+dp++mg+gp++A++kaL+kag++++d
  lcl|FitnessBrowser__Dino:3609683 234 FTK-DGS-VTAANASGLNDGAAGVLLMSAENAEKRGITPMARIASYATAGLDPSIMGVGPIYASRKALEKAGWKVDD 308
                                       *95.9*7.********************************************************************* PP

                         TIGR01930 304 idlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGa 380
                                       +dlvE nEAFAaq+ av+k++g  d++ vNvnGGAiA+GHP+GasGar++ tll e+++r++k GlatlC+ggG+G+
  lcl|FitnessBrowser__Dino:3609683 309 LDLVEANEAFAAQACAVNKDMG-WDPAIVNVNGGAIAIGHPIGASGARVLNTLLFEMQRRDAKKGLATLCIGGGMGV 384
                                       **********************.88**************************************************** PP

                         TIGR01930 381 Avile 385
                                       A+ +e
  lcl|FitnessBrowser__Dino:3609683 385 ALCVE 389
                                       *9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (391 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: 00:00:00.01
# Mc/sec: 10.26
//
[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