GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Dechlorosoma suillum PS

Align 3-ketoacyl-CoA thiolase (EC 2.3.1.16) (characterized)
to candidate Dsui_0976 Dsui_0976 acetyl-CoA acetyltransferase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_2982
         (397 letters)



>FitnessBrowser__PS:Dsui_0976
          Length = 393

 Score =  520 bits (1339), Expect = e-152
 Identities = 261/390 (66%), Positives = 319/390 (81%)

Query: 5   NDPIVIVSAVRTPMGGFQGELKSLTAPQLGAAAIKAAVERAGVASDSVDEVLFGCVLPAG 64
           +DPIVIVS  RTPMGGFQG+  SLTAPQLGA AIKAAVERAG+  + V+EV+FG VL AG
Sbjct: 2   SDPIVIVSVARTPMGGFQGDFNSLTAPQLGATAIKAAVERAGIKPEQVEEVVFGNVLQAG 61

Query: 65  LGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMSN 124
           +GQAPARQAALGAGL  S  CTT++K+CGS +++ ++ HD LLAGS ++ VAGG ESMSN
Sbjct: 62  VGQAPARQAALGAGLPLSAGCTTIHKVCGSALKSVMMVHDSLLAGSYEIGVAGGQESMSN 121

Query: 125 APYLLDRARAGYRMGHGRVQDSMFLDGLEDAYDKGRLMGTFAEDCAETNGFSREAQDAFA 184
           APYLL +AR GYR+GHG++ D MF DGLEDAY KGRLMGTFAE+CAE+ GF+REAQD +A
Sbjct: 122 APYLLPKARGGYRLGHGQLLDHMFFDGLEDAYQKGRLMGTFAEECAESYGFTREAQDEWA 181

Query: 185 IASTTRAQQAIKDGSFKAEIVPLTVTVGKEQVVISNDEQPPKARLDKIASLKPAFREGGT 244
           I ST RAQ+AIK+G FK EI P+T+   K  VV+  DEQP KA+++KI +LKPAF++ GT
Sbjct: 182 IQSTVRAQKAIKEGLFKWEIAPVTIAGKKGDVVVDQDEQPLKAQIEKIPALKPAFKKDGT 241

Query: 245 VTAANSSSISDGAAALVLMRQSQAQKQGLKPLAVIHGHAAFADTPGLFPVAPIGAIKKLM 304
           VTAANSSSISDGAAALVLM++S+A+  GL P+A I GH   A  P LF  AP+ A++KLM
Sbjct: 242 VTAANSSSISDGAAALVLMKESKAKVLGLAPIAKIVGHTTHAQEPNLFTTAPVFAMEKLM 301

Query: 305 KKTGWSLNDVDLVEVNEAFAVVGMAAMTHLEIPHEKLNVHGGACALGHPIGASGARILVT 364
           +KTGW++ DVDL E+NEAFAVV MAA+  L++   K+NVHGGACALGHPIGASGARILVT
Sbjct: 302 QKTGWNVADVDLWEINEAFAVVTMAAIKDLKLDPAKVNVHGGACALGHPIGASGARILVT 361

Query: 365 LLSALRQKGLKRGVAAICIGGGEATAMAVE 394
           L+ AL+Q G K+GVA++CIGGGEA A+ VE
Sbjct: 362 LIGALKQYGKKKGVASLCIGGGEAVAVGVE 391


Lambda     K      H
   0.318    0.132    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: 548
Number of extensions: 15
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: 397
Length of database: 393
Length adjustment: 31
Effective length of query: 366
Effective length of database: 362
Effective search space:   132492
Effective search space used:   132492
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 Dsui_0976 Dsui_0976 (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.8963.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   5.4e-134  432.9   3.4   6.1e-134  432.7   3.4    1.0  1  lcl|FitnessBrowser__PS:Dsui_0976  Dsui_0976 acetyl-CoA acetyltrans


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_0976  Dsui_0976 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  432.7   3.4  6.1e-134  6.1e-134       1     384 [.       7     390 ..       7     391 .. 0.98

  Alignments for each domain:
  == domain 1  score: 432.7 bits;  conditional E-value: 6.1e-134
                         TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpesvpal 77 
                                       iv+ +Rtp+g ++g +++l+a +L+a++ik+++erag++pe+++ev++Gnvlqag ++++aR+aal aglp s   +
  lcl|FitnessBrowser__PS:Dsui_0976   7 IVSVARTPMGGFQGDFNSLTAPQLGATAIKAAVERAGIKPEQVEEVVFGNVLQAGVGQAPARQAALGAGLPLSAGCT 83 
                                       89********99***************************************************************** PP

                         TIGR01930  78 tvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl....vktkls 150
                                       t+++vC+S+l++v+++ +++ aG +++ vaGG EsmS++p+ll+++  r +++lg+ +l d++  d+     +++  
  lcl|FitnessBrowser__PS:Dsui_0976  84 TIHKVCGSALKSVMMVHDSLLAGSYEIGVAGGQESMSNAPYLLPKA--RGGYRLGHGQLLDHMFFDGledaYQKGRL 158
                                       ********************************************98..89***********999998999988999* PP

                         TIGR01930 151 mgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpnttlekLakLkp 225
                                       mg+ Ae++a+ yg++Re qDe+a++S  +a+kAi+eg fk ei pv++ gk  ++vv++De++  + ++ek+  Lkp
  lcl|FitnessBrowser__PS:Dsui_0976 159 MGTFAEECAESYGFTREAQDEWAIQSTVRAQKAIKEGLFKWEIAPVTIAGKkgDVVVDQDEQPL-KAQIEKIPALKP 234
                                       **************************************************99888888888887.89********** PP

                         TIGR01930 226 afkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsis 302
                                       afk+ +g tvtA+Nss+++DGAaal+lm+e++ak lgl p+a+iv++++ + +p+ ++++pv A+ek+++k+g+++ 
  lcl|FitnessBrowser__PS:Dsui_0976 235 AFKK-DG-TVTAANSSSISDGAAALVLMKESKAKVLGLAPIAKIVGHTTHAQEPNLFTTAPVFAMEKLMQKTGWNVA 309
                                       **95.9*.6******************************************************************** PP

                         TIGR01930 303 didlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqG 379
                                       d+dl+EinEAFA++++a++k+l+ ld++kvNv+GGA AlGHP+GasGari++tl+ +Lk+ gkk G+a+lC+ggG +
  lcl|FitnessBrowser__PS:Dsui_0976 310 DVDLWEINEAFAVVTMAAIKDLK-LDPAKVNVHGGACALGHPIGASGARILVTLIGALKQYGKKKGVASLCIGGGEA 385
                                       ***********************.99*************************************************** PP

                         TIGR01930 380 aAvil 384
                                       +Av +
  lcl|FitnessBrowser__PS:Dsui_0976 386 VAVGV 390
                                       **966 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (393 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.50
//
[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