GapMind for catabolism of small carbon sources

 

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

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate Ac3H11_3920 Acetyl-CoA acetyltransferase (EC 2.3.1.9) @ Beta-ketoadipyl CoA thiolase (EC 2.3.1.-)

Query= metacyc::MONOMER-3207
         (400 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3920
          Length = 403

 Score =  507 bits (1305), Expect = e-148
 Identities = 261/400 (65%), Positives = 307/400 (76%), Gaps = 2/400 (0%)

Query: 2   RDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQAG 61
           R  FICDAIRTP GR+GGAL+ VR DDL A+P+KAL++ NP V W  V +VF+GCANQAG
Sbjct: 5   RQAFICDAIRTPFGRYGGALSSVRTDDLGAIPIKALMDRNPGVDWAAVTDVFYGCANQAG 64

Query: 62  EDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMS 121
           EDNRNVA M+ LLAGLP  + G T+NRLC SG+DA+GTA RAI +GE  L IAGGVESMS
Sbjct: 65  EDNRNVAHMSSLLAGLPIEVAGATINRLCGSGLDAVGTAARAIKAGEAGLMIAGGVESMS 124

Query: 122 RAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRADQ 181
           RAPFVM KAES +SRN  + DTTIGWRF+N LMK +YGVDSMPETA+NVA D+++ R  Q
Sbjct: 125 RAPFVMPKAESAFSRNSAVYDTTIGWRFVNKLMKEKYGVDSMPETAENVATDFKIEREAQ 184

Query: 182 DAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGET-IVERDEHLRPETTLEALTKLKPV 240
           D  ALRSQ  A AA  AG  A EIVPV I  KKG+  IV +DEH R ET+LEAL KLK V
Sbjct: 185 DQMALRSQLNAVAAIKAGHLAREIVPVHIPQKKGDAIIVSQDEHPR-ETSLEALAKLKGV 243

Query: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVP 300
             PD TVTAGNASGVNDGA AL+LA      K+GL PRARV+GMA  GVAPR+MG GP P
Sbjct: 244 VRPDGTVTAGNASGVNDGACALLLADEANAAKYGLKPRARVVGMAVAGVAPRIMGFGPTP 303

Query: 301 AVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM 360
           A +K+  + G+ +   DVIELNEAFA+QGLAVLR LG+ DD  +VN  GGAIALGHPLG 
Sbjct: 304 ATQKVLAQTGLTIDHMDVIELNEAFAAQGLAVLRALGLKDDDGRVNAWGGAIALGHPLGA 363

Query: 361 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           SGARLV TA+++L +  G+  L TMC+GVGQG+A+ +ERV
Sbjct: 364 SGARLVTTAVNRLHEHAGQYALCTMCIGVGQGIAVILERV 403


Lambda     K      H
   0.318    0.134    0.383 

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: 502
Number of extensions: 13
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: 400
Length of database: 403
Length adjustment: 31
Effective length of query: 369
Effective length of database: 372
Effective search space:   137268
Effective search space used:   137268
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_3920 (Acetyl-CoA acetyltransferase (EC 2.3.1.9) @ Beta-ketoadipyl CoA thiolase (EC 2.3.1.-))
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.15667.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   4.6e-134  433.1   4.9   5.2e-134  432.9   4.9    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920  Acetyl-CoA acetyltransferase (EC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920  Acetyl-CoA acetyltransferase (EC 2.3.1.9) @ Beta-ketoadipyl CoA thio
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  432.9   4.9  5.2e-134  5.2e-134       1     385 []       9     401 ..       9     401 .. 0.95

  Alignments for each domain:
  == domain 1  score: 432.9 bits;  conditional E-value: 5.2e-134
                                        TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.ani 60 
                                                      i da+Rtp+g++gg+l++++ +dL+a  ik+l++r+ g+d +++ +v +G++ qage+  n+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920   9 ICDAIRTPFGRYGGALSSVRTDDLGAIPIKALMDRNpGVDWAAVTDVFYGCANQAGEDnRNV 70 
                                                      789*******99**********************************************9*** PP

                                        TIGR01930  61 aReaalaaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillka 122
                                                      a +  l aglp +v++ t+nr+C+Sgl+Av +aa++ikaGea +++aGGvEsmSr+p+++++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920  71 AHMSSLLAGLPIEVAGATINRLCGSGLDAVGTAARAIKAGEAGLMIAGGVESMSRAPFVMPK 132
                                                      **********************************************************9999 PP

                                        TIGR01930 123 slrreslklgkakledqllkdl........vktklsmgetAenlakkygisReeqDeyalrS 176
                                                      +   es+  +++ ++d+++           ++   sm etAen+a++++i+Re qD+ alrS
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920 133 A---ESAFSRNSAVYDTTIGWRfvnklmkeKYGVDSMPETAENVATDFKIEREAQDQMALRS 191
                                                      7...44444555555533332267777887677789************************** PP

                                        TIGR01930 177 hqkaakAieegkfkdeivpvevkgk...kkvvskDegirpnttlekLakLkpafkekkgstv 235
                                                      + +a +Ai++g++++eivpv++++k   + +vs+De++r +t+le+LakLk + + ++g tv
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920 192 QLNAVAAIKAGHLAREIVPVHIPQKkgdAIIVSQDEHPR-ETSLEALAKLKGVVR-PDG-TV 250
                                                      ***********************9999999999****99.89************9.69*.6* PP

                                        TIGR01930 236 tAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkka 297
                                                      tAgN+s++nDGA+alll+ e+ a+++gl+p ar+v++avagv p++mg+gp+pA++k+L+++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920 251 TAGNASGVNDGACALLLADEANAAKYGLKPRARVVGMAVAGVAPRIMGFGPTPATQKVLAQT 312
                                                      ************************************************************** PP

                                        TIGR01930 298 glsisdidlvEinEAFAaqvlavekelgsld.lekvNvnGGAiAlGHPlGasGarivltllk 358
                                                      gl+i+ +d++E+nEAFAaq lav ++lg++d + +vN +GGAiAlGHPlGasGar+v+t ++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920 313 GLTIDHMDVIELNEAFAAQGLAVLRALGLKDdDGRVNAWGGAIALGHPLGASGARLVTTAVN 374
                                                      ****************************866799**************************** PP

                                        TIGR01930 359 eLkergkkyGlatlCvggGqGaAvile 385
                                                      +L+e+ ++y+l t+C+g GqG+Avile
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3920 375 RLHEHAGQYALCTMCIGVGQGIAVILE 401
                                                      *************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (403 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: 12.53
//
[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