Alignments for a candidate for fadA in Novosphingobium barchaimii LL02

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Novosphingobium barchaimii LL02

Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate WP_059150441.1 V474_RS05390 acetyl-CoA C-acyltransferase

Query= SwissProt::Q0KBP1
         (394 letters)



>NCBI__GCF_001046635.1:WP_059150441.1
          Length = 393

 Score =  446 bits (1148), Expect = e-130
 Identities = 222/391 (56%), Positives = 278/391 (71%), Gaps = 1/391 (0%)

Query: 4   EVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQTEPR 63
           E+ +VSGVRTA+G FGGSLK   P++LGALV  EAL RA +  + V HVV G V+ T  R
Sbjct: 3   EIYIVSGVRTAVGDFGGSLKSFMPSDLGALVAAEALKRAGIEAEAVEHVVIGQVMPTSAR 62

Query: 64  DMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESMSRA 123
           D  L RV  +  G+ +  PALT+NRLCGSG+QAI+S+AQ + LG+  V + GGAE MS  
Sbjct: 63  DQTLSRVIGIKAGIPLATPALTLNRLCGSGVQAIISSAQMMKLGEASVTLAGGAEVMSNV 122

Query: 124 PYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAALES 183
           PY     RWG +MG     D +   L D     HMG+TAENVA+ + +SR   D  A  S
Sbjct: 123 PYHDHGVRWGKKMGANTQEDALTLGLSDAIGEYHMGITAENVAERHHVSREDMDALAATS 182

Query: 184 HRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKENGTV 243
           H RA+ AI  G FKDQI+PV  K RKG   FDTDEHVR D T + + K++P F K++G V
Sbjct: 183 HSRAARAIAEGRFKDQILPVEVKTRKGVTVFDTDEHVRADTTPETLAKMKPAF-KKDGLV 241

Query: 244 TAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKIALE 303
           TAGNASG+ND AAAVV+    E E+RGLKPLAR+V++GHAGV+P+ MG GP+ A  IAL+
Sbjct: 242 TAGNASGINDGAAAVVLATGTEVEKRGLKPLARIVAWGHAGVEPEYMGEGPIVAVPIALK 301

Query: 304 RAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALITVKA 363
           RAGL +  +D+IE+NEAFAAQACAV +ALG DP KVNPNGSG+S+GHP+GATG ++T+K 
Sbjct: 302 RAGLTLDQIDIIESNEAFAAQACAVARALGFDPEKVNPNGSGVSIGHPVGATGTMLTIKC 361

Query: 364 LHELNRVQGRYALVTMCIGGGQGIAAIFERI 394
            +EL R  GRY LVTMCIGGGQGIA + E +
Sbjct: 362 AYELKRTGGRYGLVTMCIGGGQGIALVIENV 392


Lambda     K      H
   0.318    0.134    0.381 

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: 467
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: 394
Length of database: 393
Length adjustment: 31
Effective length of query: 363
Effective length of database: 362
Effective search space:   131406
Effective search space used:   131406
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_059150441.1 V474_RS05390 (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.3990322.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.4e-138  447.2   6.1   2.7e-138  447.0   6.1    1.0  1  NCBI__GCF_001046635.1:WP_059150441.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001046635.1:WP_059150441.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  447.0   6.1  2.7e-138  2.7e-138       1     385 []       6     390 ..       6     390 .. 0.97

  Alignments for each domain:
  == domain 1  score: 447.0 bits;  conditional E-value: 2.7e-138
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaaglpe 72 
                                           iv++vRt++g +ggslk+++++dL+a v  e+l+rag+++e++++v++G+v+++++  +++ R + ++ag+p 
  NCBI__GCF_001046635.1:WP_059150441.1   6 IVSGVRTAVGDFGGSLKSFMPSDLGALVAAEALKRAGIEAEAVEHVVIGQVMPTSARdQTLSRVIGIKAGIPL 78 
                                           8*****************************************************9999*************** PP

                             TIGR01930  73 svpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl. 144
                                            +palt+nr+C+Sg+qA+++ aq+ k Gea+v +aGG+E mS+vp+  +    r++ k+g++++ed+l+  + 
  NCBI__GCF_001046635.1:WP_059150441.1  79 ATPALTLNRLCGSGVQAIISSAQMMKLGEASVTLAGGAEVMSNVPYHDHG--VRWGKKMGANTQEDALTL-Gl 148
                                           *********************************************97766..49***********95444.45 PP

                             TIGR01930 145 ..vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirp 213
                                             +  +++mg+tAen+a+++++sRe++D++a+ Sh++aa+Ai+eg+fkd+i+pvevk++   +v+++De++r+
  NCBI__GCF_001046635.1:WP_059150441.1 149 sdAIGEYHMGITAENVAERHHVSREDMDALAATSHSRAARAIAEGRFKDQILPVEVKTRkgVTVFDTDEHVRA 221
                                           987799***************************************************999999********** PP

                             TIGR01930 214 nttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgp 286
                                           +tt e+Lak+kpafk+ +g  vtAgN+s++nDGAaa++l++ + +++ gl+plariv++++agv+pe+mg gp
  NCBI__GCF_001046635.1:WP_059150441.1 222 DTTPETLAKMKPAFKK-DG-LVTAGNASGINDGAAAVVLATGTEVEKRGLKPLARIVAWGHAGVEPEYMGEGP 292
                                           **************95.9*.5**************************************************** PP

                             TIGR01930 287 vpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllke 359
                                           + A++ aLk+agl++++id++E nEAFAaq+ av+++lg  d+ekvN nG+ +++GHP+Ga+G++++++ ++e
  NCBI__GCF_001046635.1:WP_059150441.1 293 IVAVPIALKRAGLTLDQIDIIESNEAFAAQACAVARALG-FDPEKVNPNGSGVSIGHPVGATGTMLTIKCAYE 364
                                           ***************************************.78******************************* PP

                             TIGR01930 360 LkergkkyGlatlCvggGqGaAvile 385
                                           Lk+ g++yGl+t+C+ggGqG+A+++e
  NCBI__GCF_001046635.1:WP_059150441.1 365 LKRTGGRYGLVTMCIGGGQGIALVIE 390
                                           ************************97 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 25.26
//
[ok]

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

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Protein sequences (fasta format)
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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