Alignments for a candidate for fadA in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Dechlorosoma suillum PS

Align 3-ketoacyl-CoA thiolase FadI; ACSs; Acetyl-CoA acyltransferase; Acyl-CoA ligase; Beta-ketothiolase; Fatty acid oxidation complex subunit beta; EC 2.3.1.16 (characterized)
to candidate Dsui_0325 Dsui_0325 acetyl-CoA acetyltransferase

Query= SwissProt::P76503
         (436 letters)



>FitnessBrowser__PS:Dsui_0325
          Length = 432

 Score =  233 bits (593), Expect = 1e-65
 Identities = 143/424 (33%), Positives = 222/424 (52%), Gaps = 7/424 (1%)

Query: 15  IAIVSGLRTPFARQATAFHGIPAVDLGKMVVGELLARSEIPAEVIEQLVFGQVVQMPEAP 74
           + +V G RTPF +         A DL       LLAR     E ++++V G     P+  
Sbjct: 10  VYVVDGARTPFLKAKNGPGPFSAADLAVQAGRALLARQPFAPEDLDEVVLGCASPSPDEV 69

Query: 75  NIAREIVLGTGMNVHTDAYSVSRACATSFQAVANVAESLMAGTIRAGIAGGADSSSVLPI 134
           NI R   L  G       ++V R CA+  QA+ +   ++ +G     +AGG D+ S  P+
Sbjct: 70  NIGRVAALRLGCGNKVTGWTVMRNCASGMQALDSAMANIQSGRSELVLAGGVDALSRAPL 129

Query: 135 GVSKKLARVLVDVNKARTMSQRLKLFSRLR----LRDLMPVPPAVAEYSTGLRMGDTAEQ 190
             +  +      + + +T+ Q+   F +LR    L  ++ +   + +   GL MG TAE 
Sbjct: 130 LYNDAMVLWFAGMMQMKTLGQKAGHFLKLRPSVLLNPVIGLMKGLTDPVVGLLMGQTAEN 189

Query: 191 MAKTYGITREQQDALAHRSHQRAAQAWSDGKLKEEVMTAFIPPYKQPLVEDNNIRGNSSL 250
           +A  +GI+RE+ DA + RSHQR     +     E V    +        ED+ +R ++S+
Sbjct: 190 LAWRFGISREEMDAFSVRSHQRVMAGRAKQAFGEIV--PLVGNDGTVYAEDDGVRVDASM 247

Query: 251 ADYAKLRPAFDRKHGTVTAANSTPLTDGAAAVILMTESRAKELGLVPLGYLRSYAFTAID 310
               KL+P FD+K+G VT ANS+ +TDG A ++L +ES  K   L PLG +    +  +D
Sbjct: 248 DGMKKLKPFFDKKYGRVTPANSSQITDGGAWLLLASESAVKRWKLEPLGRIVDAQWAGLD 307

Query: 311 VWQDMLLGPAWSTPLALERAGLTMSDLTLIDMHEAFAAQTLANIQLLGSERFAREALGRA 370
             Q M LGP  +    L+R GL ++D+ L++++EAFAAQ L  ++    + + RE LG  
Sbjct: 308 PSQ-MGLGPVHAVTPILQRHGLGLNDVDLMEINEAFAAQVLGCLKAWEDDAYCREELGLP 366

Query: 371 HATGEVDDSKFNVLGGSIAYGHPFAATGARMITQTLHELRRRGGGFGLVTACAAGGLGAA 430
            A G +D  K NV GG++A GHP  A+GAR++   LH L+ RGG  G+ + C  GG G A
Sbjct: 367 GALGSLDQDKLNVDGGAVAQGHPVGASGARIVLHLLHALKARGGKRGVASICIGGGQGGA 426

Query: 431 MVLE 434
           M++E
Sbjct: 427 MLVE 430


Lambda     K      H
   0.319    0.133    0.377 

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: 462
Number of extensions: 18
Number of successful extensions: 4
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: 436
Length of database: 432
Length adjustment: 32
Effective length of query: 404
Effective length of database: 400
Effective search space:   161600
Effective search space used:   161600
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate Dsui_0325 Dsui_0325 (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.8307.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.3e-128  415.2   0.0   1.4e-128  415.0   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_0325  Dsui_0325 acetyl-CoA acetyltrans


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_0325  Dsui_0325 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  415.0   0.0  1.4e-128  1.4e-128       1     385 []      12     430 ..      12     430 .. 0.96

  Alignments for each domain:
  == domain 1  score: 415.0 bits;  conditional E-value: 1.4e-128
                         TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpesvpal 77 
                                       +vd++Rtp+ k+++    +sa+dL++++ ++ll+r+ + pe++dev+lG++ ++ +++ni+R aal+ g++++v ++
  lcl|FitnessBrowser__PS:Dsui_0325  12 VVDGARTPFLKAKNGPGPFSAADLAVQAGRALLARQPFAPEDLDEVVLGCASPSPDEVNIGRVAALRLGCGNKVTGW 88 
                                       79*********9***************************************************************** PP

                         TIGR01930  78 tvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.......... 144
                                       tv r CaSg+qA+ +a+++i++G+ ++v+aGGv+ +Sr+p+l ++++  + + + ++k+  q++ ++          
  lcl|FitnessBrowser__PS:Dsui_0325  89 TVMRNCASGMQALDSAMANIQSGRSELVLAGGVDALSRAPLLYNDAMVLWFAGMMQMKTLGQKAGHFlklrpsvlln 165
                                       *********************************************9887777776666666555555899******* PP

                         TIGR01930 145 ...........vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgkkkvvskDeg 210
                                                  +  +l mg+tAenla+++gisRee+D++++rShq+  +  ++  f  eivp++ ++  +v+++D+g
  lcl|FitnessBrowser__PS:Dsui_0325 166 pviglmkgltdPVVGLLMGQTAENLAWRFGISREEMDAFSVRSHQRVMAGRAKQAFG-EIVPLVGND-GTVYAEDDG 240
                                       ***********889*********************************9999988885.899998887.7999***** PP

                         TIGR01930 211 irpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpv 287
                                       +r + +++ ++kLkp f++k g+ vt +Nssq++DG a lll+se+++k+ +l+pl+riv+a++ag+dp++mglgpv
  lcl|FitnessBrowser__PS:Dsui_0325 241 VRVDASMDGMKKLKPFFDKKYGR-VTPANSSQITDGGAWLLLASESAVKRWKLEPLGRIVDAQWAGLDPSQMGLGPV 316
                                       **********************6.***************************************************** PP

                         TIGR01930 288 pAiekaLkkaglsisdidlvEinEAFAaqvlavekelgs................ldlekvNvnGGAiAlGHPlGas 348
                                       +A++ +L+++gl ++d+dl+EinEAFAaqvl + k++++                ld++k+Nv GGA+A GHP+Gas
  lcl|FitnessBrowser__PS:Dsui_0325 317 HAVTPILQRHGLGLNDVDLMEINEAFAAQVLGCLKAWEDdaycreelglpgalgsLDQDKLNVDGGAVAQGHPVGAS 393
                                       *****************************************************9877******************** PP

                         TIGR01930 349 GarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                       Garivl+ll++Lk rg+k+G+a++C+ggGqG A+++e
  lcl|FitnessBrowser__PS:Dsui_0325 394 GARIVLHLLHALKARGGKRGVASICIGGGQGGAMLVE 430
                                       **********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (432 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: 8.99
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources