Alignments for a candidate for fadA in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Escherichia coli BW25113

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.16) (characterized)
to candidate 16925 b2844 putative acyltransferase (VIMSS)

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



>FitnessBrowser__Keio:16925
          Length = 393

 Score =  530 bits (1364), Expect = e-155
 Identities = 257/392 (65%), Positives = 327/392 (83%), Gaps = 1/392 (0%)

Query: 1   MQDVVIVAATRTAVGSFQGSLASIPAPELGAAVIRRLLEQTGLDPAQVDEVILGQVLTAG 60
           M+DVVIV A RT +G F+G+LA   A ELG+ V++ L+E+TG+    VDEVILGQVLTAG
Sbjct: 1   MKDVVIVGALRTPIGCFRGALAGHSAVELGSLVVKALIERTGVPAYAVDEVILGQVLTAG 60

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

Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREAQDAFAA 180
           AP+VL  +RTG ++G+++++DS++ DGLWDAFNDYH+G+TAENL  +YGISR+ QDA+A 
Sbjct: 121 APHVLTDSRTGAQLGNSQLVDSLVHDGLWDAFNDYHIGVTAENLAREYGISRQLQDAYAL 180

Query: 181 ASQQKATAAIEAGRFVDEITPILIPQRKGDPVAFAVDEQPRAGTTAESLAKLKPAFKKDG 240
           +SQQKA AAI+AGRF DEI P++  Q  G  +    DEQPR   +AE LA+L P+F   G
Sbjct: 181 SSQQKARAAIDAGRFKDEIVPVMT-QSNGQTLVVDTDEQPRTDASAEGLARLNPSFDSLG 239

Query: 241 SVTAGNASSLNDGAAAVLLMSADKAKALGLPVLARIASYANAGVDPAIMGIGPVSATRRC 300
           SVTAGNASS+NDGAAAV++MS  KA+AL LPVLARI ++A+ GVDPA+MGI PV ATRRC
Sbjct: 240 SVTAGNASSINDGAAAVMMMSEAKARALNLPVLARIRAFASVGVDPALMGIAPVYATRRC 299

Query: 301 LDKAGWSLGDLDLIEANEAFAAQSLAVGKELEWDAEKVNVNGGAIAIGHPIGASGCRVLV 360
           L++ GW L ++DLIEANEAFAAQ+L+VGK LEWD  +VNVNGGAIA+GHPIGASGCR+LV
Sbjct: 300 LERVGWQLAEVDLIEANEAFAAQALSVGKMLEWDERRVNVNGGAIALGHPIGASGCRILV 359

Query: 361 TLLHEMIKRDAKKGLATLCIGGGQGVALALER 392
           +L+HEM+KR+A+KGLATLCIGGGQGVAL +ER
Sbjct: 360 SLVHEMVKRNARKGLATLCIGGGQGVALTIER 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: 468
Number of extensions: 13
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: 393
Length adjustment: 31
Effective length of query: 362
Effective length of database: 362
Effective search space:   131044
Effective search space used:   131044
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 16925 b2844 (putative acyltransferase (VIMSS))
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.24794.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   6.6e-145  468.8   6.1   7.5e-145  468.6   6.1    1.0  1  lcl|FitnessBrowser__Keio:16925  b2844 putative acyltransferase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:16925  b2844 putative acyltransferase (VIMSS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  468.6   6.1  7.5e-145  7.5e-145       1     385 []       6     390 ..       6     390 .. 0.99

  Alignments for each domain:
  == domain 1  score: 468.6 bits;  conditional E-value: 7.5e-145
                       TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpesvpaltv 79 
                                     iv+a+Rtpig ++g+l+  sa++L++ v+k+l+er+g+ + ++devilG+vl+ag+++n+aR+ a++ glp+sv+a+t+
  lcl|FitnessBrowser__Keio:16925   6 IVGALRTPIGCFRGALAGHSAVELGSLVVKALIERTGVPAYAVDEVILGQVLTAGAGQNPARQSAIKGGLPNSVSAITI 84 
                                     89********99******************************************************************* PP

                       TIGR01930  80 nrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl...vktklsmgetA 155
                                     n vC+Sgl+A++la q+i++Gead+v+aGG E+mSr+p++l +s  r +++lg+++l d+l++d+   + ++++ g+tA
  lcl|FitnessBrowser__Keio:16925  85 NDVCGSGLKALHLATQAIQCGEADIVIAGGQENMSRAPHVLTDS--RTGAQLGNSQLVDSLVHDGlwdAFNDYHIGVTA 161
                                     ******************************************98..89********************99********* PP

                       TIGR01930 156 enlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpnttlekLakLkpafkekkg 232
                                     enla++ygisR+ qD+yal+S+qka +Ai++g+fkdeivpv  + +  + vv++De++r + ++e La+L+p f++  g
  lcl|FitnessBrowser__Keio:16925 162 ENLAREYGISRQLQDAYALSSQQKARAAIDAGRFKDEIVPVMTQSNgqTLVVDTDEQPRTDASAEGLARLNPSFDS-LG 239
                                     *****************************************9999999999***********************96.89 PP

                       TIGR01930 233 stvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinE 311
                                     s vtAgN+s++nDGAaa+++mse++a++l+l +lari+++a +gvdp+ mg++pv+A++++L++ g+++ ++dl+E nE
  lcl|FitnessBrowser__Keio:16925 240 S-VTAGNASSINDGAAAVMMMSEAKARALNLPVLARIRAFASVGVDPALMGIAPVYATRRCLERVGWQLAEVDLIEANE 317
                                     7.***************************************************************************** PP

                       TIGR01930 312 AFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                     AFAaq+l v k l+  d+ +vNvnGGAiAlGHP+GasG+ri+++l++e+ +r+++ GlatlC+ggGqG+A+ +e
  lcl|FitnessBrowser__Keio:16925 318 AFAAQALSVGKMLE-WDERRVNVNGGAIALGHPIGASGCRILVSLVHEMVKRNARKGLATLCIGGGQGVALTIE 390
                                     **************.88*****************************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (393 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: 8.87
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources