GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Marinobacter adhaerens HP15

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.16) (characterized)
to candidate GFF3052 HP15_2996 acetyl-CoA acetyltransferase

Query= metacyc::MONOMER-20831
         (393 letters)



>FitnessBrowser__Marino:GFF3052
          Length = 398

 Score =  552 bits (1422), Expect = e-162
 Identities = 270/392 (68%), Positives = 330/392 (84%)

Query: 1   MQDVVIVAATRTAVGSFQGSLASIPAPELGAAVIRRLLEQTGLDPAQVDEVILGQVLTAG 60
           M+DVVIVAA RTA+G+F G L+S+ A +LG AVI+ +LE+TG+   Q++EV+LGQVLTAG
Sbjct: 7   MRDVVIVAARRTAIGTFGGGLSSLSADQLGTAVIKAILEETGVAGDQINEVVLGQVLTAG 66

Query: 61  SGQNPARQASILAGLPHAVPSLTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120
            GQNPARQ++I AG+P +VP++T+NKVCGSGLKA+H+  QAIRCGDAE++IAGG E+MS 
Sbjct: 67  CGQNPARQSAINAGIPASVPAMTINKVCGSGLKAVHMAVQAIRCGDAEMMIAGGQESMSQ 126

Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREAQDAFAA 180
           AP+VLP +R G RMG+  M+D+MI DGLWDAFNDYHMGITAEN+V+KYGISR+ QD FAA
Sbjct: 127 APHVLPNSRNGQRMGNWSMVDTMIKDGLWDAFNDYHMGITAENIVEKYGISRDEQDEFAA 186

Query: 181 ASQQKATAAIEAGRFVDEITPILIPQRKGDPVAFAVDEQPRAGTTAESLAKLKPAFKKDG 240
           ASQQKA AA EAG F  +I P+ IPQRKGDP+    DE PR G TAE L KL+ AFKKDG
Sbjct: 187 ASQQKAAAAREAGYFDGQIVPVSIPQRKGDPIVVDRDEGPRDGVTAEGLGKLRAAFKKDG 246

Query: 241 SVTAGNASSLNDGAAAVLLMSADKAKALGLPVLARIASYANAGVDPAIMGIGPVSATRRC 300
           +VTAGNASSLNDGAAAV++ SA+KA+ LGL  +A I +YANAGVDP IMG GP+ A++RC
Sbjct: 247 TVTAGNASSLNDGAAAVMVCSAEKAEELGLTPIATIKAYANAGVDPTIMGTGPIPASQRC 306

Query: 301 LDKAGWSLGDLDLIEANEAFAAQSLAVGKELEWDAEKVNVNGGAIAIGHPIGASGCRVLV 360
           L  AGWS  DLDL+EANEAFAAQ+++V +++ WD  KVNVNGGAIA+GHPIGASGCR+LV
Sbjct: 307 LKLAGWSTEDLDLVEANEAFAAQAISVNRDMGWDTGKVNVNGGAIALGHPIGASGCRILV 366

Query: 361 TLLHEMIKRDAKKGLATLCIGGGQGVALALER 392
           +LLHEM++RD  KGLATLCIGGG GVALA+ER
Sbjct: 367 SLLHEMVRRDVHKGLATLCIGGGMGVALAVER 398


Lambda     K      H
   0.317    0.133    0.378 

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: 505
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: 393
Length of database: 398
Length adjustment: 31
Effective length of query: 362
Effective length of database: 367
Effective search space:   132854
Effective search space used:   132854
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 GFF3052 HP15_2996 (acetyl-CoA acetyltransferase)
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.2351212.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.1e-149  482.3   7.7   5.8e-149  482.1   7.7    1.0  1  lcl|FitnessBrowser__Marino:GFF3052  HP15_2996 acetyl-CoA acetyltrans


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF3052  HP15_2996 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  482.1   7.7  5.8e-149  5.8e-149       1     385 []      12     397 ..      12     397 .. 0.99

  Alignments for each domain:
  == domain 1  score: 482.1 bits;  conditional E-value: 5.8e-149
                           TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpesvp 75 
                                         iv+a Rt+ig++gg l++lsa++L++avik++le +g+  ++i+ev+lG+vl+ag+++n+aR+ a++ag+p svp
  lcl|FitnessBrowser__Marino:GFF3052  12 IVAARRTAIGTFGGGLSSLSADQLGTAVIKAILEETGVAGDQINEVVLGQVLTAGCGQNPARQSAINAGIPASVP 86 
                                         89************************************************************************* PP

                           TIGR01930  76 altvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl...vkt 147
                                         a+t+n+vC+Sgl+Av++a+q+i++G+a++++aGG EsmS++p++l++s  r++ ++g+ ++ d+++kd+   + +
  lcl|FitnessBrowser__Marino:GFF3052  87 AMTINKVCGSGLKAVHMAVQAIRCGDAEMMIAGGQESMSQAPHVLPNS--RNGQRMGNWSMVDTMIKDGlwdAFN 159
                                         ***********************************************8..89********************99* PP

                           TIGR01930 148 klsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...kkvvskDegirpnttlek 219
                                         +++mg+tAen+ +kygisR+eqDe+a++S+qkaa+A e+g+f+ +ivpv+++++   + vv++Deg+r+++t+e 
  lcl|FitnessBrowser__Marino:GFF3052 160 DYHMGITAENIVEKYGISRDEQDEFAAASQQKAAAAREAGYFDGQIVPVSIPQRkgdPIVVDRDEGPRDGVTAEG 234
                                         ****************************************************999*99***************** PP

                           TIGR01930 220 LakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaL 294
                                         L+kL++afk+ +g tvtAgN+s+lnDGAaa+++ s e+a+elgltp+a+i ++a+agvdp++mg+gp+pA++++L
  lcl|FitnessBrowser__Marino:GFF3052 235 LGKLRAAFKK-DG-TVTAGNASSLNDGAAAVMVCSAEKAEELGLTPIATIKAYANAGVDPTIMGTGPIPASQRCL 307
                                         ********95.9*.6************************************************************ PP

                           TIGR01930 295 kkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGl 369
                                         k ag+s++d+dlvE nEAFAaq++ v++++g  d+ kvNvnGGAiAlGHP+GasG+ri+++ll+e+ +r+++ Gl
  lcl|FitnessBrowser__Marino:GFF3052 308 KLAGWSTEDLDLVEANEAFAAQAISVNRDMG-WDTGKVNVNGGAIALGHPIGASGCRILVSLLHEMVRRDVHKGL 381
                                         *******************************.88***************************************** PP

                           TIGR01930 370 atlCvggGqGaAvile 385
                                         atlC+ggG+G+A+ +e
  lcl|FitnessBrowser__Marino:GFF3052 382 ATLCIGGGMGVALAVE 397
                                         ************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (398 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: 26.80
//
[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