GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Klebsiella michiganensis M5al

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.16) (characterized)
to candidate BWI76_RS23445 BWI76_RS23445 acetyl-CoA acetyltransferase

Query= metacyc::MONOMER-20831
         (393 letters)



>FitnessBrowser__Koxy:BWI76_RS23445
          Length = 391

 Score =  533 bits (1374), Expect = e-156
 Identities = 260/392 (66%), Positives = 328/392 (83%), Gaps = 1/392 (0%)

Query: 1   MQDVVIVAATRTAVGSFQGSLASIPAPELGAAVIRRLLEQTGLDPAQVDEVILGQVLTAG 60
           M+DVVIV A RT +G FQG+L+   A ELG+ V++ L+E++G+DP  +DEVILGQVLTAG
Sbjct: 1   MKDVVIVGALRTPIGCFQGTLSRHSAVELGSVVVKALVERSGVDPQSIDEVILGQVLTAG 60

Query: 61  SGQNPARQASILAGLPHAVPSLTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120
           +GQNPARQ++I  GLP+ V ++T+N VCGSGLKALHL  QAI+CG+A+V+IAGG ENMS 
Sbjct: 61  TGQNPARQSAIRGGLPNTVSAITINDVCGSGLKALHLATQAIQCGEADVVIAGGQENMSR 120

Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREAQDAFAA 180
           AP+VL  +RTG ++G++++IDS++ DGLWDAFNDYHMG+TAENL  +YGISRE QDA+A 
Sbjct: 121 APHVLTDSRTGAQLGNSQLIDSLVHDGLWDAFNDYHMGVTAENLAREYGISRELQDAWAL 180

Query: 181 ASQQKATAAIEAGRFVDEITPILIPQRKGDPVAFAVDEQPRAGTTAESLAKLKPAFKKDG 240
           +SQ KA  AI++GRF DEI P+   +  G P     DEQPR   +AE+LA L P F + G
Sbjct: 181 SSQHKARRAIDSGRFRDEIVPVT-SELNGIPRLVDTDEQPRVDPSAEALASLLPTFDQQG 239

Query: 241 SVTAGNASSLNDGAAAVLLMSADKAKALGLPVLARIASYANAGVDPAIMGIGPVSATRRC 300
           SVTAGNASS+NDGAAAV++MS  KA+ALGLP+LARI ++A+ GVDPA+MGI PV ATRRC
Sbjct: 240 SVTAGNASSINDGAAAVMMMSETKAEALGLPILARIRAFASVGVDPALMGIAPVHATRRC 299

Query: 301 LDKAGWSLGDLDLIEANEAFAAQSLAVGKELEWDAEKVNVNGGAIAIGHPIGASGCRVLV 360
           L++AGW L ++DLIEANEAFAAQ+++VG+ LEWD  +VNVNGGAIA+GHPIGASGCR+LV
Sbjct: 300 LERAGWKLDEVDLIEANEAFAAQAISVGRVLEWDERRVNVNGGAIALGHPIGASGCRILV 359

Query: 361 TLLHEMIKRDAKKGLATLCIGGGQGVALALER 392
           +L+HEMIKRDA+KGLATLCIGGGQGVALA+ER
Sbjct: 360 SLVHEMIKRDARKGLATLCIGGGQGVALAVER 391


Lambda     K      H
   0.317    0.133    0.378 

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: 471
Number of extensions: 16
Number of successful extensions: 2
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: 391
Length adjustment: 31
Effective length of query: 362
Effective length of database: 360
Effective search space:   130320
Effective search space used:   130320
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 BWI76_RS23445 BWI76_RS23445 (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.13699.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   2.1e-147  477.0   1.4   2.3e-147  476.9   1.4    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS23445  BWI76_RS23445 acetyl-CoA acetylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS23445  BWI76_RS23445 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  476.9   1.4  2.3e-147  2.3e-147       1     385 []       6     390 ..       6     390 .. 0.99

  Alignments for each domain:
  == domain 1  score: 476.9 bits;  conditional E-value: 2.3e-147
                               TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglp 71 
                                             iv+a+Rtpig ++g+l+  sa++L++ v+k+l+er+g+dp+ idevilG+vl+ag+++n+aR+ a++ glp
  lcl|FitnessBrowser__Koxy:BWI76_RS23445   6 IVGALRTPIGCFQGTLSRHSAVELGSVVVKALVERSGVDPQSIDEVILGQVLTAGTGQNPARQSAIRGGLP 76 
                                             89********99*********************************************************** PP

                               TIGR01930  72 esvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllk 142
                                             ++v+a+t+n vC+Sgl+A++la q+i++Geadvv+aGG E+mSr+p++l +s  r +++lg+++l d+l++
  lcl|FitnessBrowser__Koxy:BWI76_RS23445  77 NTVSAITINDVCGSGLKALHLATQAIQCGEADVVIAGGQENMSRAPHVLTDS--RTGAQLGNSQLIDSLVH 145
                                             **************************************************98..89*************** PP

                               TIGR01930 143 dl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskD 208
                                             d+   + ++++mg+tAenla++ygisRe qD++al+S++ka +Ai++g+f deivpv+ + +  ++ v++D
  lcl|FitnessBrowser__Koxy:BWI76_RS23445 146 DGlwdAFNDYHMGVTAENLAREYGISRELQDAWALSSQHKARRAIDSGRFRDEIVPVTSELNgiPRLVDTD 216
                                             *****99****************************************************999********* PP

                               TIGR01930 209 egirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdp 279
                                             e++r + ++e+La+L p f++ +gs vtAgN+s++nDGAaa+++mse++a++lgl +lari+++a +gvdp
  lcl|FitnessBrowser__Koxy:BWI76_RS23445 217 EQPRVDPSAEALASLLPTFDQ-QGS-VTAGNASSINDGAAAVMMMSETKAEALGLPILARIRAFASVGVDP 285
                                             *******************95.8*7.********************************************* PP

                               TIGR01930 280 eemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGa 350
                                             + mg++pv+A++++L++ag++++++dl+E nEAFAaq++ v + l+  d+ +vNvnGGAiAlGHP+GasG+
  lcl|FitnessBrowser__Koxy:BWI76_RS23445 286 ALMGIAPVHATRRCLERAGWKLDEVDLIEANEAFAAQAISVGRVLE-WDERRVNVNGGAIALGHPIGASGC 355
                                             **********************************************.88********************** PP

                               TIGR01930 351 rivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                             ri+++l++e+ +r+++ GlatlC+ggGqG+A+ +e
  lcl|FitnessBrowser__Koxy:BWI76_RS23445 356 RILVSLVHEMIKRDARKGLATLCIGGGQGVALAVE 390
                                             *******************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (391 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: 10.91
//
[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