GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__PS:Dsui_0976 Dsui_0976 acetyl-CoA
           acetyltransferase
          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.6846.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.55
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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