GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Koxy:BWI76_RS23445 BWI76_RS23445 acetyl-CoA
           acetyltransferase
          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.32699.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 9.45
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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