Alignments for a candidate for fadA in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Stenotrophomonas chelatiphaga DSM 21508

Align 3-ketoacyl-CoA thiolase; EC 2.3.1.16; ACSs; Acetyl-CoA acyltransferase; Acyl-CoA ligase; Beta-ketothiolase; Fatty acid oxidation complex subunit beta (uncharacterized)
to candidate WP_057509233.1 ABB28_RS14140 acetyl-CoA C-acyltransferase

Query= curated2:B7UFZ9
         (436 letters)



>NCBI__GCF_001431535.1:WP_057509233.1
          Length = 426

 Score =  287 bits (735), Expect = 4e-82
 Identities = 167/427 (39%), Positives = 247/427 (57%), Gaps = 15/427 (3%)

Query: 15  IAIVSGLRTPFARQATAFHGIPAGDLGKMV--VGELLARTEIPAEVIEQLVFGQVVQMPE 72
           +AI+ G+R PF RQ TA+  +  G+LG  V  +G L+ R  +  + + ++  G V++   
Sbjct: 7   VAILGGVRIPFCRQNTAYSDV--GNLGMSVRTLGALVERFGLHGQQLGEVAMGAVIKHSS 64

Query: 73  APNIAREIVLGTGMNVHTDAYSVSRACATSFQAVANVAESLMAGTIRAGIAGGADSSSVL 132
             N+ RE  L +G++  T   ++ RAC TS   +  VA  +  G I +GI GG+D++S +
Sbjct: 65  DWNLGREAALSSGLSPLTPGITMQRACGTSLDTIIAVANKIALGQIESGIGGGSDTTSDV 124

Query: 133 PIGVSKKLARVLVDVNKARTMSQRLKLFSR-LRLRDLMPVPPAVAEYSTGLRMGDTAEQM 191
           PI   KKL   L+  N+A++   +++  +R  +  +  P  P VAE  TG  MGD  E M
Sbjct: 125 PIVYGKKLRARLLAANRAKSTGDKIRALTRGFKFSEFKPEFPGVAEPRTGKSMGDHCEDM 184

Query: 192 AKTYGITREQQDALAHRSHQRAAQAWSEGKLKEEVMTAFIPPYKQPLVEDNNIRGNSSLA 251
           AK + I+R+ QD  A  SH++ A A+  G   +      I P++  +  DN +R ++SL 
Sbjct: 185 AKEWNISRDSQDEWAVSSHRKLAAAYERGFFND-----LIAPFRG-VERDNILRADTSLE 238

Query: 252 DYAKLRPAFDRK--HGTVTAANSTPLTDGAAAVILMTESRAKELGLVPLGYLRSYAFTAI 309
             A L+PAFD+    GT+TAANSTPLTDGA+AV+L +E  A+  G  PL YLR     A+
Sbjct: 239 KLATLKPAFDKVSGRGTLTAANSTPLTDGASAVLLASEEWARAHGHAPLAYLRDSQVAAV 298

Query: 310 DV--WQDMLLGPAWSTPLALERAGLTMSDLTLIDMHEAFAAQTLANIQLLGSERFARDVL 367
           D    + +L+ P  + P  L+R GLT+ D  + ++HEAFAAQ L  ++   SE + R+ L
Sbjct: 299 DFVHGEGLLMAPTVAVPEMLKRNGLTLQDFDIYEIHEAFAAQVLCTLRAWESEDYCRNRL 358

Query: 368 GRAHATGEVDDSKFNVLGGSIAYGHPFAATGARMITQTLHELRRRGGGFGLVTACAAGGL 427
           G     G +D  K N LG S+A GHPFAATGAR+I     +L  RGGG  LV+ C AGG+
Sbjct: 359 GLDAPLGRIDPEKINPLGSSLATGHPFAATGARVIATAAKQLAERGGGRALVSICTAGGM 418

Query: 428 GAAMVLE 434
           G   ++E
Sbjct: 419 GVVAIVE 425


Lambda     K      H
   0.319    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: 444
Number of extensions: 24
Number of successful extensions: 5
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: 436
Length of database: 426
Length adjustment: 32
Effective length of query: 404
Effective length of database: 394
Effective search space:   159176
Effective search space used:   159176
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_057509233.1 ABB28_RS14140 (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.5946.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-118  379.9   0.0   7.4e-118  379.7   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057509233.1  ABB28_RS14140 acetyl-CoA C-acylt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057509233.1  ABB28_RS14140 acetyl-CoA C-acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  379.7   0.0  7.4e-118  7.4e-118       1     385 []       9     425 ..       9     425 .. 0.97

  Alignments for each domain:
  == domain 1  score: 379.7 bits;  conditional E-value: 7.4e-118
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 
                                               i+++vR+p+++++++++++ +  +++ ++ +l+er+gl+ +++ ev++G+v++++++ n++Reaal++g
  lcl|NCBI__GCF_001431535.1:WP_057509233.1   9 ILGGVRIPFCRQNTAYSDVGNLGMSVRTLGALVERFGLHGQQLGEVAMGAVIKHSSDWNLGREAALSSG 77 
                                               789*******99********************************************************* PP

                                 TIGR01930  70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138
                                               l+  +p++t++r+C+++l++++ +a+ki+ G+++  + GG +++S+vpi+  ++lr++ l  ++ak+  
  lcl|NCBI__GCF_001431535.1:WP_057509233.1  78 LSPLTPGITMQRACGTSLDTIIAVANKIALGQIESGIGGGSDTTSDVPIVYGKKLRARLLAANRAKSTG 146
                                               ********************************************************9999999999888 PP

                                 TIGR01930 139 qllkdl..................vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkf 189
                                                +++ l                  ++t+ smg + e +ak+++isR++qDe+a++Sh+k a+A+e+g+f
  lcl|NCBI__GCF_001431535.1:WP_057509233.1 147 DKIRALtrgfkfsefkpefpgvaePRTGKSMGDHCEDMAKEWNISRDSQDEWAVSSHRKLAAAYERGFF 215
                                               77777789****************9******************************************** PP

                                 TIGR01930 190 kdeivpvevkgkkkvvskDegirpnttlekLakLkpafkekkgs.tvtAgNssqlnDGAaalllmseev 257
                                               +d i p+  +g    v++D+ +r++t+lekLa+Lkpaf++ +g+ t tA+Ns++l+DGA+a+ll+see+
  lcl|NCBI__GCF_001431535.1:WP_057509233.1 216 NDLIAPF--RG----VERDNILRADTSLEKLATLKPAFDKVSGRgTLTAANSTPLTDGASAVLLASEEW 278
                                               ******5..54....689**********************666558*********************** PP

                                 TIGR01930 258 akelgltplarivsaavagvdp...eemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlaveke 323
                                               a+++g  pla++++ +va+vd    e ++++p+ A++++Lk++gl+++d+d++Ei+EAFAaqvl   ++
  lcl|NCBI__GCF_001431535.1:WP_057509233.1 279 ARAHGHAPLAYLRDSQVAAVDFvhgEGLLMAPTVAVPEMLKRNGLTLQDFDIYEIHEAFAAQVLCTLRA 347
                                               *********************9999******************************************** PP

                                 TIGR01930 324 lgs................ldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvgg 376
                                               ++s                +d+ek+N  G+++A+GHP++a+Gar+++t +k+L+erg+ ++l+++C +g
  lcl|NCBI__GCF_001431535.1:WP_057509233.1 348 WESedycrnrlgldaplgrIDPEKINPLGSSLATGHPFAATGARVIATAAKQLAERGGGRALVSICTAG 416
                                               *****************9877************************************************ PP

                                 TIGR01930 377 GqGaAvile 385
                                               G+G+ +i+e
  lcl|NCBI__GCF_001431535.1:WP_057509233.1 417 GMGVVAIVE 425
                                               ***999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (426 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: 9.57
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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