Alignments for a candidate for fadA in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Dyella japonica UNC79MFTsu3.2

Align 3-ketoacyl-CoA thiolase [isoleucine degradation] (EC 2.3.1.16) (characterized)
to candidate N515DRAFT_0938 N515DRAFT_0938 acetyl-CoA C-acetyltransferase

Query= reanno::MR1:200842
         (396 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0938
          Length = 394

 Score =  473 bits (1217), Expect = e-138
 Identities = 242/388 (62%), Positives = 300/388 (77%), Gaps = 2/388 (0%)

Query: 10  IVIVAAKRTPMGSFQGSLSGITSLSLAATAIKALLADTQVAPDKVDEVLMGCVLPAGLGQ 69
           +VI  AKRT +GSF G  +G+ +  L ATAIKA L    +A   V+EVLMGCVLPA LGQ
Sbjct: 6   VVIAGAKRTAIGSFLGQFTGVPTPVLGATAIKAALEQAGIAAQDVNEVLMGCVLPANLGQ 65

Query: 70  APARQATLGAGLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSAKVVIAGGMESMSQAPY 129
           APARQA L AGLP +VG TTVNKVCGSGMK +ML HDLIKAGSA VV+AGGMESM+ AP+
Sbjct: 66  APARQAALKAGLPAAVGCTTVNKVCGSGMKAIMLGHDLIKAGSAAVVVAGGMESMTNAPH 125

Query: 130 LLDKARAGIRMGHGKVLDHMFLDGLEDAYTGGAMGTFAQKTADEFGITREQMDAFALSSL 189
           +++ AR GIR G G+++DHM  DGL + Y G AMG F +  AD++  TRE+ DAFA+ S+
Sbjct: 126 MVN-ARTGIRYGDGQLVDHMAWDGLTNPYDGKAMGVFGELCADKYHFTREEQDAFAIESV 184

Query: 190 EKANAAINSGAFKTEIVPVTVSDRRGDVTIDTDEQPGNARPEKIPTLRPAFAKD-GTITA 248
           ++A AA  +GAF  EIVPVTV+ R+GDV +DTDEQPG +   K+P+L+PAF K+ GTITA
Sbjct: 185 KRAQAAQQNGAFAGEIVPVTVAGRKGDVVVDTDEQPGRSDIAKVPSLKPAFRKENGTITA 244

Query: 249 ANSSSISDGAAALMLTTRANAEQLGLTVLATIKGHTTHAQEPALFTTAPVGAMAKLLSNV 308
           A+SSSISDGAAA++L +  +A+  GL  LA I  H TH+QEP  FTTAPV A+ K+L   
Sbjct: 245 ASSSSISDGAAAVVLLSADDAKARGLQPLARIVAHATHSQEPEWFTTAPVSAIQKVLDKA 304

Query: 309 GWSKDEVDLFEINEAFAMVTMLAVSELGLDMTKVNVNGGACALGHPIGCSGARLLVTLIH 368
           GW  D+VDLFE+NEAFA+V M  + ELG+   K+NVNGGACALGHPIG SG RL+VTL++
Sbjct: 305 GWKVDDVDLFEVNEAFAVVAMAPMRELGIPHAKLNVNGGACALGHPIGASGTRLVVTLLN 364

Query: 369 ALKARGLKRGVASLCIGGGEATAMAIEV 396
           AL+ RGLKRGVASLCIGGGEATA+A+E+
Sbjct: 365 ALQTRGLKRGVASLCIGGGEATAIAVEL 392


Lambda     K      H
   0.316    0.131    0.364 

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: 507
Number of extensions: 15
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: 396
Length of database: 394
Length adjustment: 31
Effective length of query: 365
Effective length of database: 363
Effective search space:   132495
Effective search space used:   132495
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate N515DRAFT_0938 N515DRAFT_0938 (acetyl-CoA C-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.12581.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.2e-129  418.6   8.6   1.4e-129  418.3   8.6    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0938  N515DRAFT_0938 acetyl-CoA C-acet


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0938  N515DRAFT_0938 acetyl-CoA C-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  418.3   8.6  1.4e-129  1.4e-129       1     385 []       8     391 ..       8     391 .. 0.98

  Alignments for each domain:
  == domain 1  score: 418.3 bits;  conditional E-value: 1.4e-129
                                    TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaal 66 
                                                  i +a Rt+ig++ g++  ++   L+a++ik++le+ag+ +++++ev +G+vl+a+ ++++aR+aal
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0938   8 IAGAKRTAIGSFLGQFTGVPTPVLGATAIKAALEQAGIAAQDVNEVLMGCVLPANLGQAPARQAAL 73 
                                                  7789************************************************************** PP

                                    TIGR01930  67 aaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklg 132
                                                  +aglp  v  +tvn+vC+Sg++A++l+ + ikaG a vvvaGG+Esm+++p++++a+    ++++g
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0938  74 KAGLPAAVGCTTVNKVCGSGMKAIMLGHDLIKAGSAAVVVAGGMESMTNAPHMVNAR---TGIRYG 136
                                                  ****************************************************99985...89**** PP

                                    TIGR01930 133 kakledqllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivp 195
                                                  + +l d+++ d+   ++++ +mg+  e +a+ky+++ReeqD++a++S ++a++A+++g f+ eivp
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0938 137 DGQLVDHMAWDGltnPYDGKAMGVFGELCADKYHFTREEQDAFAIESVKRAQAAQQNGAFAGEIVP 202
                                                  ******99999999999************************************************* PP

                                    TIGR01930 196 vevkgk..kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevak 259
                                                  v+v g+  ++vv++De++  ++ ++k+ +Lkpaf++++g t+tA++ss+++DGAaa++l s + ak
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0938 203 VTVAGRkgDVVVDTDEQPG-RSDIAKVPSLKPAFRKENG-TITAASSSSISDGAAAVVLLSADDAK 266
                                                  *****99888888888875.9******************.6************************* PP

                                    TIGR01930 260 elgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelg 325
                                                  + gl+plariv++a+ + +pe ++++pv Ai+k+L+kag++++d+dl+E+nEAFA++++a ++elg
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0938 267 ARGLQPLARIVAHATHSQEPEWFTTAPVSAIQKVLDKAGWKVDDVDLFEVNEAFAVVAMAPMRELG 332
                                                  ****************************************************************** PP

                                    TIGR01930 326 sldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                                   + ++k+NvnGGA AlGHP+GasG+r+v+tll++L+ rg k+G+a+lC+ggG ++A+ +e
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0938 333 -IPHAKLNVNGGACALGHPIGASGTRLVVTLLNALQTRGLKRGVASLCIGGGEATAIAVE 391
                                                  .88*****************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (394 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.16
//
[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