Alignments for a candidate for fadA in Thauera aminoaromatica S2

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Thauera aminoaromatica S2

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_004300924.1 C665_RS04210 acetyl-CoA C-acyltransferase

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



>NCBI__GCF_000310185.1:WP_004300924.1
          Length = 427

 Score =  255 bits (651), Expect = 2e-72
 Identities = 165/431 (38%), Positives = 239/431 (55%), Gaps = 39/431 (9%)

Query: 2   RDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQAG 61
           + ++I D  RTP  +   A     A DLA     AL+   P    DQ+DEV  GCA+ + 
Sbjct: 3   KPIYIVDGARTPFLKAKNAPGPFTASDLATAAGSALLMRQPFAP-DQLDEVILGCASPSA 61

Query: 62  EDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMS 121
            D  N+ R+  L  G    +PG T+ R CASGM AI +A   +  G  +L +AGGV+++S
Sbjct: 62  -DEVNIGRVVALRLGCGNKVPGWTVMRNCASGMQAIDSAIANLQCGRSQLVLAGGVDALS 120

Query: 122 RAPFVMGK-----------AESGYSRNMKLEDTTIGWRFINPLMKSQYGVDS------MP 164
            AP +  +           A S   R   L    +G   + P++    G+        M 
Sbjct: 121 HAPLLFSEKMVRWLAGWYAARSTGDRLAMLRTFRLG--HLAPVIGIMKGLTDPIVGQLMG 178

Query: 165 ETADNVADDYQVSRADQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEH 224
           +T +N+A  + ++R D DAFA+ S ++  A Q AG +AEEIVP  +  + G+ +   D+ 
Sbjct: 179 QTGENLAWKFGITREDMDAFAVESHRRVCAGQDAGHYAEEIVP--LIDRDGQ-VYAADDG 235

Query: 225 LRPETTLEALTKLKPV-NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLG 283
           +R ++++  L KLKP  +     VT GN+S + DGAA L+LAS EAV++HGL P  R++ 
Sbjct: 236 VRRDSSMANLAKLKPFFDRKYGRVTPGNSSQITDGAAWLVLASQEAVERHGLQPLGRIVD 295

Query: 284 MASGGVAPRVMGIGPVPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLR--------- 334
               G+AP  MG+GPV A   + +R G+A  D D  ELNEAFA+Q +A LR         
Sbjct: 296 SQWAGLAPDQMGLGPVHATMPILQRHGLAPDDLDAWELNEAFAAQVIACLRAFADDDYCR 355

Query: 335 -ELGV----ADDAPQVNPNGGAIALGHPLGMSGARLVLTALHQLEKSGGRKGLATMCVGV 389
              GV    A DA ++N +GGA+ALGHP+G SGAR+VL  L  L + GG +GLA++C+G 
Sbjct: 356 THFGVDAPGAPDAARLNVDGGAVALGHPVGASGARIVLHLLEVLRRKGGGRGLASICIGG 415

Query: 390 GQGLALAIERV 400
           GQG A+ +E V
Sbjct: 416 GQGGAMLVETV 426


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: 466
Number of extensions: 30
Number of successful extensions: 6
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: 427
Length adjustment: 31
Effective length of query: 369
Effective length of database: 396
Effective search space:   146124
Effective search space used:   146124
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_004300924.1 C665_RS04210 (acetyl-CoA C-acyltransferase)
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.22252.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.9e-131  423.1   0.0   5.6e-131  422.9   0.0    1.0  1  lcl|NCBI__GCF_000310185.1:WP_004300924.1  C665_RS04210 acetyl-CoA C-acyltr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000310185.1:WP_004300924.1  C665_RS04210 acetyl-CoA C-acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.9   0.0  5.6e-131  5.6e-131       1     385 []       7     424 ..       7     424 .. 0.97

  Alignments for each domain:
  == domain 1  score: 422.9 bits;  conditional E-value: 5.6e-131
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 
                                               ivd++Rtp+ k++++   ++a+dL++a+ ++ll+r+ + p+++devilG++ ++++++ni+R +al+ g
  lcl|NCBI__GCF_000310185.1:WP_004300924.1   7 IVDGARTPFLKAKNAPGPFTASDLATAAGSALLMRQPFAPDQLDEVILGCASPSADEVNIGRVVALRLG 75 
                                               8******************************************************************** PP

                                 TIGR01930  70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138
                                               ++++vp++tv r CaSg+qA+ +a +++++G+ ++v+aGGv+ +S++p+l ++++ r+ +   +a++  
  lcl|NCBI__GCF_000310185.1:WP_004300924.1  76 CGNKVPGWTVMRNCASGMQAIDSAIANLQCGRSQLVLAGGVDALSHAPLLFSEKMVRWLAGWYAARSTG 144
                                               *******************************************************99999888777777 PP

                                 TIGR01930 139 qllkdl....................vktklsmgetAenlakkygisReeqDeyalrShqkaakAieeg 187
                                                +l  l                    +  +  mg+t enla+k+gi+Re++D++a++Sh++  + +++g
  lcl|NCBI__GCF_000310185.1:WP_004300924.1 145 DRLAMLrtfrlghlapvigimkgltdPIVGQLMGQTGENLAWKFGITREDMDAFAVESHRRVCAGQDAG 213
                                               666666788****************988999************************************** PP

                                 TIGR01930 188 kfkdeivpvevkgkkkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmsee 256
                                               + ++eivp+  ++  +v++ D+g+r+++++++LakLkp f++k g+ vt gNssq++DGAa l+l+s+e
  lcl|NCBI__GCF_000310185.1:WP_004300924.1 214 HYAEEIVPLIDRD-GQVYAADDGVRRDSSMANLAKLKPFFDRKYGR-VTPGNSSQITDGAAWLVLASQE 280
                                               ********86665.899****************************6.********************** PP

                                 TIGR01930 257 vakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelg 325
                                               +++++gl+pl+riv+ ++ag+ p++mglgpv+A+  +L+++gl  +d+d++E+nEAFAaqv+a+ ++++
  lcl|NCBI__GCF_000310185.1:WP_004300924.1 281 AVERHGLQPLGRIVDSQWAGLAPDQMGLGPVHATMPILQRHGLAPDDLDAWELNEAFAAQVIACLRAFA 349
                                               ********************************************************************* PP

                                 TIGR01930 326 s...............ldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqG 379
                                               +                d +++Nv GGA+AlGHP+GasGarivl+ll+ L+++g+ +Gla++C+ggGqG
  lcl|NCBI__GCF_000310185.1:WP_004300924.1 350 DddycrthfgvdapgaPDAARLNVDGGAVALGHPVGASGARIVLHLLEVLRRKGGGRGLASICIGGGQG 418
                                               ************99864499************************************************* PP

                                 TIGR01930 380 aAvile 385
                                                A+++e
  lcl|NCBI__GCF_000310185.1:WP_004300924.1 419 GAMLVE 424
                                               ***997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (427 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: 12.81
//
[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:

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