GapMind for catabolism of small carbon sources

 

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

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate Ac3H11_2303 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

Query= SwissProt::P14611
         (393 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2303
          Length = 392

 Score =  560 bits (1444), Expect = e-164
 Identities = 281/392 (71%), Positives = 330/392 (84%)

Query: 1   MTDVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAG 60
           M D+VIVSAARTAVGKFGG+LAK PA ELGA+VI+ A+ RAG+  +Q+ EVIMGQVL AG
Sbjct: 1   MEDIVIVSAARTAVGKFGGALAKTPASELGAIVIREAIARAGLSSDQIGEVIMGQVLAAG 60

Query: 61  SGQNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMSA 120
            GQNPARQA++KAG+    PA+TIN VCGSGLKAVMLAA A+  GD++IVVAGGQENMS 
Sbjct: 61  VGQNPARQASMKAGVAKETPALTINAVCGSGLKAVMLAAQAVAWGDSDIVVAGGQENMSL 120

Query: 121 APHVLPGSRDGFRMGDAKLVDTMIVDGLWDVYNQYHMGITAENVAKEYGITREAQDEFAV 180
           APHVL GSRDG RMGD K+VD+MIVDGLWDVYNQYHMGITAENVAK YGITR+ QD  A+
Sbjct: 121 APHVLNGSRDGQRMGDWKMVDSMIVDGLWDVYNQYHMGITAENVAKAYGITRDMQDALAL 180

Query: 181 GSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLKPAFDKAG 240
           GSQ KA AAQ AGKF +EIV V + Q+KGDP+ F  DE++ +    ++++GL+PAFDKAG
Sbjct: 181 GSQQKAAAAQDAGKFADEIVGVSLAQKKGDPILFNADEYLNRKTNAEALAGLRPAFDKAG 240

Query: 241 TVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGPVPASKRA 300
           +VTA NASGLNDGAAAVVVMSA KA  LGL PLA I ++  +G+DP  MGMGPVPAS++A
Sbjct: 241 SVTAGNASGLNDGAAAVVVMSAKKAAALGLKPLARIAAFGTSGLDPATMGMGPVPASRKA 300

Query: 301 LSRAEWTPQDLDLMEINEAFAAQALAVHQQMGWDTSKVNVNGGAIAIGHPIGASGCRILV 360
           L RA W   D+DL E+NEAFAAQA AV++++  D +KVNVNGGAIAIGHPIGASGCRILV
Sbjct: 301 LQRAGWNAADVDLFELNEAFAAQACAVNKELAIDPAKVNVNGGAIAIGHPIGASGCRILV 360

Query: 361 TLLHEMKRRDAKKGLASLCIGGGMGVALAVER 392
           TLLHEM+RRDAKKGLA+LCIGGGMGV+LA+ER
Sbjct: 361 TLLHEMQRRDAKKGLAALCIGGGMGVSLALER 392


Lambda     K      H
   0.315    0.131    0.369 

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: 532
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: 393
Length of database: 392
Length adjustment: 31
Effective length of query: 362
Effective length of database: 361
Effective search space:   130682
Effective search space used:   130682
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate Ac3H11_2303 (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.6999.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-145  469.1  14.7   6.1e-145  468.9  14.7    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2303  3-ketoacyl-CoA thiolase (EC 2.3.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2303  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 !  468.9  14.7  6.1e-145  6.1e-145       1     385 []       6     391 ..       6     391 .. 0.99

  Alignments for each domain:
  == domain 1  score: 468.9 bits;  conditional E-value: 6.1e-145
                                        TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaR 62 
                                                      iv+a+Rt++gk+gg+l++++a++L+a vi+e+++ragl+ ++i evi+G+vl ag ++n+aR
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2303   6 IVSAARTAVGKFGGALAKTPASELGAIVIREAIARAGLSSDQIGEVIMGQVLAAGVGQNPAR 67 
                                                      8************************************************************* PP

                                        TIGR01930  63 eaalaaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkasl 124
                                                      +a ++ag+ +++palt+n vC+Sgl+Av+laaq+++ G+ d+vvaGG E+mS +p++l+ s 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2303  68 QASMKAGVAKETPALTINAVCGSGLKAVMLAAQAVAWGDSDIVVAGGQENMSLAPHVLNGS- 128
                                                      ***********************************************************98. PP

                                        TIGR01930 125 rreslklgkakledqllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakA 183
                                                       r++ ++g+ k+ d+++ d+   v+++++mg+tAen+ak ygi+R++qD++al S+qkaa+A
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2303 129 -RDGQRMGDWKMVDSMIVDGlwdVYNQYHMGITAENVAKAYGITRDMQDALALGSQQKAAAA 189
                                                      .8*****************9***99************************************* PP

                                        TIGR01930 184 ieegkfkdeivpvevkgk...kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssq 242
                                                      +++gkf+deiv v++ +k   +  ++ De + ++t++e+La+L+paf++ +gs vtAgN+s+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2303 190 QDAGKFADEIVGVSLAQKkgdPILFNADEYLNRKTNAEALAGLRPAFDK-AGS-VTAGNASG 249
                                                      ***************99999999************************95.9*7.******** PP

                                        TIGR01930 243 lnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdi 304
                                                      lnDGAaa+++ms ++a++lgl+plari +++++g+dp++mg+gpvpA++kaL++ag+++ d+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2303 250 LNDGAAAVVVMSAKKAAALGLKPLARIAAFGTSGLDPATMGMGPVPASRKALQRAGWNAADV 311
                                                      ************************************************************** PP

                                        TIGR01930 305 dlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkk 366
                                                      dl+E+nEAFAaq+ av+kel+ +d++kvNvnGGAiA+GHP+GasG+ri++tll+e+++r++k
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2303 312 DLFELNEAFAAQACAVNKELA-IDPAKVNVNGGAIAIGHPIGASGCRILVTLLHEMQRRDAK 372
                                                      *********************.88************************************** PP

                                        TIGR01930 367 yGlatlCvggGqGaAvile 385
                                                       Gla+lC+ggG+G+++ le
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2303 373 KGLAALCIGGGMGVSLALE 391
                                                      **************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (392 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: 00:00:00.02
# Mc/sec: 7.20
//
[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