GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Lacinutrix algicola AKS293

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_055435026.1 ASC41_RS02340 3-oxoadipyl-CoA thiolase

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



>NCBI__GCF_001418085.1:WP_055435026.1
          Length = 404

 Score =  415 bits (1066), Expect = e-120
 Identities = 209/402 (51%), Positives = 286/402 (71%), Gaps = 2/402 (0%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           M++ +I D IRTPIG + G L+ VR DDL A+ +  +++ NP++  +  D+V  GCANQA
Sbjct: 1   MKEAYIIDGIRTPIGNYKGTLSAVRTDDLGALVISEIVKRNPSIPKEAYDDVIMGCANQA 60

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           GEDNRNVARM+ LLAGLP ++PG T+NRLC+SG+ AI  A RAI +G+ ++ I+GGVE+M
Sbjct: 61  GEDNRNVARMSSLLAGLPFTVPGETVNRLCSSGLSAIIHANRAIKAGDGDVFISGGVENM 120

Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180
           +R P+VM K  + +  + K+ D+T GWRFINP M++ YG D M  TA+N+ + Y +SR D
Sbjct: 121 TRGPYVMAKPSTAFGGDSKMYDSTFGWRFINPKMQALYGTDGMGNTAENLVEKYNISRED 180

Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETI-VERDEHLRPETTLEALTKLKP 239
           QD FAL SQQKA  AQ +G  A+EIV V I  +K + I   +DE ++P ++LE L KL+ 
Sbjct: 181 QDKFALWSQQKATKAQESGRLAKEIVTVEIPQRKKDPIQFSKDEFIKPTSSLEVLGKLRA 240

Query: 240 V-NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGP 298
                  +VTAGN+SG+NDGAAA I+ASA+AVKK+ L P AR++  A  GV PR+MGIGP
Sbjct: 241 AFKKEGGSVTAGNSSGLNDGAAATIIASADAVKKYNLKPLARIVSSAVVGVEPRIMGIGP 300

Query: 299 VPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPL 358
           V A  K   + G+ + D D+IELNEAFA+Q LA +R  G+AD+ P++NPNGGAIA+GHPL
Sbjct: 301 VQASNKALAKAGLTMDDIDIIELNEAFAAQALACIRAWGIADNDPRINPNGGAIAIGHPL 360

Query: 359 GMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           G++GAR+  +A  +L+    +  L TMC+GVGQG A  IE V
Sbjct: 361 GVTGARVAHSAALELQNQNKKYALITMCIGVGQGYAAIIENV 402


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: 429
Number of extensions: 16
Number of successful extensions: 3
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: 404
Length adjustment: 31
Effective length of query: 369
Effective length of database: 373
Effective search space:   137637
Effective search space used:   137637
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 WP_055435026.1 ASC41_RS02340 (3-oxoadipyl-CoA thiolase)
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.3155216.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.1e-142  459.6   1.1   4.6e-142  459.4   1.1    1.0  1  NCBI__GCF_001418085.1:WP_055435026.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001418085.1:WP_055435026.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  459.4   1.1  4.6e-142  4.6e-142       1     385 []       6     400 ..       6     400 .. 0.96

  Alignments for each domain:
  == domain 1  score: 459.4 bits;  conditional E-value: 4.6e-142
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaalaaglp 71 
                                           i+d++Rtpig+++g+l+ ++ +dL+a vi+e+++r+  + +e+ d+vi+G++ qage+  n+aR+  l aglp
  NCBI__GCF_001418085.1:WP_055435026.1   6 IIDGIRTPIGNYKGTLSAVRTDDLGALVISEIVKRNpSIPKEAYDDVIMGCANQAGEDnRNVARMSSLLAGLP 78 
                                           89********99************************999999****************9************** PP

                             TIGR01930  72 esvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl 144
                                            +vp+ tvnr+C+Sgl A++ a ++ikaG+ dv+++GGvE+m+r p+++ +    +++  g++k++d++   +
  NCBI__GCF_001418085.1:WP_055435026.1  79 FTVPGETVNRLCSSGLSAIIHANRAIKAGDGDVFISGGVENMTRGPYVMAKP---STAFGGDSKMYDST---F 145
                                           ***********************************************99987...45555677777744...2 PP

                             TIGR01930 145 ...........vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...kk 203
                                                       +    mg+tAenl +ky+isRe+qD++al S+qka+kA+e+g++++eiv ve++++   + 
  NCBI__GCF_001418085.1:WP_055435026.1 146 gwrfinpkmqaLYGTDGMGNTAENLVEKYNISREDQDKFALWSQQKATKAQESGRLAKEIVTVEIPQRkkdPI 218
                                           34578888888778889*************************************************9999999 PP

                             TIGR01930 204 vvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavag 276
                                           ++skDe i+p+++le L+kL++afk++ gs vtAgNss+lnDGAaa++++s +++k+++l+plarivs av+g
  NCBI__GCF_001418085.1:WP_055435026.1 219 QFSKDEFIKPTSSLEVLGKLRAAFKKEGGS-VTAGNSSGLNDGAAATIIASADAVKKYNLKPLARIVSSAVVG 290
                                           9************************99996.****************************************** PP

                             TIGR01930 277 vdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsld.lekvNvnGGAiAlGHPlGas 348
                                           v+p++mg+gpv+A++kaL+kagl+++did++E+nEAFAaq+la+++++g  d + ++N nGGAiA+GHPlG++
  NCBI__GCF_001418085.1:WP_055435026.1 291 VEPRIMGIGPVQASNKALAKAGLTMDDIDIIELNEAFAAQALACIRAWGIADnDPRINPNGGAIAIGHPLGVT 363
                                           *************************************************877899****************** PP

                             TIGR01930 349 GarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                           Gar+  + + eL++++kky+l+t+C+g GqG A+i+e
  NCBI__GCF_001418085.1:WP_055435026.1 364 GARVAHSAALELQNQNKKYALITMCIGVGQGYAAIIE 400
                                           ***********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (404 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 17.40
//
[ok]

This GapMind analysis is from Sep 24 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