GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Acidovorax sp. GW101-3H11

Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate Ac3H11_178 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

Query= SwissProt::Q0KBP1
         (394 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_178
          Length = 394

 Score =  608 bits (1567), Expect = e-178
 Identities = 305/394 (77%), Positives = 338/394 (85%)

Query: 1   MTREVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQT 60
           MTREVVVVS VRTAIGTFGGSLKD+AP +LGALVV+E+LARA V G DVGHVVFG+V+ T
Sbjct: 1   MTREVVVVSAVRTAIGTFGGSLKDIAPTDLGALVVKESLARASVEGKDVGHVVFGHVVNT 60

Query: 61  EPRDMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESM 120
           EP+DMYL RVAA+NGG     PA  VNRLCGSGLQAIVSAAQ I LGD DV IG GAE M
Sbjct: 61  EPKDMYLSRVAAINGGCAEGTPAFNVNRLCGSGLQAIVSAAQAIQLGDADVTIGAGAEVM 120

Query: 121 SRAPYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAA 180
           SRAP+ +   RWGARMGD  +VDMM+GALHDPFH IHMGVTAEN+A ++ ISR  QD+ A
Sbjct: 121 SRAPFASLNMRWGARMGDTKMVDMMIGALHDPFHTIHMGVTAENIAAKWGISREDQDKLA 180

Query: 181 LESHRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKEN 240
           +ESH RA  A  AGYFKDQIVPV  K +KGDV + TDEH R  AT+DD  KL+PVFVKEN
Sbjct: 181 VESHNRAERATAAGYFKDQIVPVTLKSKKGDVQYATDEHFRPGATLDDFAKLKPVFVKEN 240

Query: 241 GTVTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKI 300
           GTVTAGNASG+NDAAAAVV+M+ A A+ RG KPLARLV+Y HAGVDPK MGIGPVPAT++
Sbjct: 241 GTVTAGNASGINDAAAAVVLMDAAAAKARGAKPLARLVAYAHAGVDPKYMGIGPVPATQL 300

Query: 301 ALERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALIT 360
           AL++AGL V+DLDVIEANEAFAAQACAVTK LGLDPAKVNPNGSGISLGHPIGATGALIT
Sbjct: 301 ALKKAGLTVADLDVIEANEAFAAQACAVTKDLGLDPAKVNPNGSGISLGHPIGATGALIT 360

Query: 361 VKALHELNRVQGRYALVTMCIGGGQGIAAIFERI 394
           VKA+HEL RVQGRYALVTMCIGGGQGIAAIFER+
Sbjct: 361 VKAIHELQRVQGRYALVTMCIGGGQGIAAIFERL 394


Lambda     K      H
   0.318    0.134    0.381 

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: 569
Number of extensions: 7
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: 394
Length of database: 394
Length adjustment: 31
Effective length of query: 363
Effective length of database: 363
Effective search space:   131769
Effective search space used:   131769
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 Ac3H11_178 (3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9))
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.6801.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
     9e-141  455.2   8.5     1e-140  455.0   8.5    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_178  3-ketoacyl-CoA thiolase (EC 2.3.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_178  3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase 
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  455.0   8.5    1e-140    1e-140       1     385 []       7     392 ..       7     392 .. 0.99

  Alignments for each domain:
  == domain 1  score: 455.0 bits;  conditional E-value: 1e-140
                                       TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaR 62 
                                                     +v+avRt+ig++ggslk++ + dL+a v+ke l+ra ++ +++ +v++G+v+++  + + + R
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_178   7 VVSAVRTAIGTFGGSLKDIAPTDLGALVVKESLARASVEGKDVGHVVFGHVVNTEPKdMYLSR 69 
                                                     79***************************************************99998***** PP

                                       TIGR01930  63 eaalaaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslr 125
                                                      aa++ g+ e +pa++vnr+C+SglqA+ +aaq+i+ G+adv + +G+E mSr+p+ + +   
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_178  70 VAAINGGCAEGTPAFNVNRLCGSGLQAIVSAAQAIQLGDADVTIGAGAEVMSRAPFASLNM-- 130
                                                     *******************************************************998886.. PP

                                       TIGR01930 126 reslklgkakledqllkdl..vktklsmgetAenlakkygisReeqDeyalrShqkaakAiee 186
                                                     r+++++g++k+ d+++  l  + + ++mg+tAen+a+k+gisRe+qD++a++Sh++a++A+++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_178 131 RWGARMGDTKMVDMMIGALhdPFHTIHMGVTAENIAAKWGISREDQDKLAVESHNRAERATAA 193
                                                     8************9999989999**************************************** PP

                                       TIGR01930 187 gkfkdeivpvevkgk..kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGA 247
                                                     g+fkd+ivpv++k k  ++++++De+ rp+ tl++ akLkp+f +++g tvtAgN+s++nD+A
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_178 194 GYFKDQIVPVTLKSKkgDVQYATDEHFRPGATLDDFAKLKPVFVKENG-TVTAGNASGINDAA 255
                                                     *************99999999***************************.6************* PP

                                       TIGR01930 248 aalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEin 310
                                                     aa++lm  ++ak+ g +plar+v++a+agvdp++mg+gpvpA++ aLkkagl++ d+d++E n
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_178 256 AAVVLMDAAAAKARGAKPLARLVAYAHAGVDPKYMGIGPVPATQLALKKAGLTVADLDVIEAN 318
                                                     *************************************************************** PP

                                       TIGR01930 311 EAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlC 373
                                                     EAFAaq+ av+k+lg ld++kvN nG+ i+lGHP+Ga+Ga i+++ ++eL++ +++y+l+t+C
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_178 319 EAFAAQACAVTKDLG-LDPAKVNPNGSGISLGHPIGATGALITVKAIHELQRVQGRYALVTMC 380
                                                     ***************.99********************************************* PP

                                       TIGR01930 374 vggGqGaAvile 385
                                                     +ggGqG+A+i+e
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_178 381 IGGGQGIAAIFE 392
                                                     **********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (394 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: 8.57
//
[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