Alignments for a candidate for fadA in Rhodobacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Rhodobacter sphaeroides ATCC 17029

Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate WP_043827862.1 RSPH17029_RS00115 acetyl-CoA C-acyltransferase

Query= SwissProt::Q0KBP1
         (394 letters)



>NCBI__GCF_000015985.1:WP_043827862.1
          Length = 389

 Score =  444 bits (1142), Expect = e-129
 Identities = 232/391 (59%), Positives = 279/391 (71%), Gaps = 4/391 (1%)

Query: 4   EVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQTEPR 63
           +++V+S VRTAIG FGG+L  V P +L   V R AL RA V    VGHVVFG+VI TEPR
Sbjct: 3   DILVLSAVRTAIGGFGGALAAVPPGDLATTVTRAALERAGVEPGRVGHVVFGHVINTEPR 62

Query: 64  DMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESMSRA 123
           DMYL RVAA+  G+    PA+ VNRLCGSG+QAIVSA Q ++LGD +VA+ GGAESMSRA
Sbjct: 63  DMYLSRVAAMQAGIPSEVPAMNVNRLCGSGVQAIVSAMQALMLGDAEVALAGGAESMSRA 122

Query: 124 PYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAALES 183
           PY    ARWG +MGD   +DMM GAL+ PF   HMG+TAE VA+ + ISR  QD  ALES
Sbjct: 123 PYALTTARWGQKMGDTRALDMMTGALNCPFGTGHMGITAEIVAERHGISREDQDAFALES 182

Query: 184 HRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKENGTV 243
             R + A + G F  QIVPV    RKG V+F  DEH +   T++ +  LRP F K  GTV
Sbjct: 183 QTRTARAQEEGRFDGQIVPVEIASRKGPVSFSRDEHPK-ATTLEALAGLRPAFQK-GGTV 240

Query: 244 TAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKIALE 303
           TAGNASG+ND A A+++    E    G +PL RL+ Y HAGVDP+ MG+GP+PA +    
Sbjct: 241 TAGNASGINDGAGALILAR--EGAVPGARPLGRLIGYAHAGVDPEVMGLGPIPAVQALCA 298

Query: 304 RAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALITVKA 363
           R GL V+D DVIE+NEAFAAQA AV +AL  DPA+VNPNG  I+LGHP+GATGA+ITVKA
Sbjct: 299 RTGLSVADFDVIESNEAFAAQALAVARALDFDPARVNPNGGAIALGHPVGATGAIITVKA 358

Query: 364 LHELNRVQGRYALVTMCIGGGQGIAAIFERI 394
           LHEL+R  GR ALVTMCIGGGQGIA   ER+
Sbjct: 359 LHELHRTGGRRALVTMCIGGGQGIALALERV 389


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: 544
Number of extensions: 20
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: 394
Length of database: 389
Length adjustment: 31
Effective length of query: 363
Effective length of database: 358
Effective search space:   129954
Effective search space used:   129954
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_043827862.1 RSPH17029_RS00115 (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.13060.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-133  431.1   5.6   2.1e-133  430.9   5.6    1.0  1  lcl|NCBI__GCF_000015985.1:WP_043827862.1  RSPH17029_RS00115 acetyl-CoA C-a


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015985.1:WP_043827862.1  RSPH17029_RS00115 acetyl-CoA C-acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  430.9   5.6  2.1e-133  2.1e-133       1     385 []       6     387 ..       6     387 .. 0.97

  Alignments for each domain:
  == domain 1  score: 430.9 bits;  conditional E-value: 2.1e-133
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaa 68 
                                               +++avRt+ig +gg+l+ +++ dL+++v +++lerag++p ++ +v++G+v+++    + + R aa++a
  lcl|NCBI__GCF_000015985.1:WP_043827862.1   6 VLSAVRTAIGGFGGALAAVPPGDLATTVTRAALERAGVEPGRVGHVVFGHVINTEPRdMYLSRVAAMQA 74 
                                               689*******99*****************************************99988*********** PP

                                 TIGR01930  69 glpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakle 137
                                               g+p++vpa++vnr+C+Sg+qA+ +a+q+++ G+a+v++aGG+EsmSr+p+ l  +  r++ k+g+++  
  lcl|NCBI__GCF_000015985.1:WP_043827862.1  75 GIPSEVPAMNVNRLCGSGVQAIVSAMQALMLGDAEVALAGGAESMSRAPYALTTA--RWGQKMGDTRAL 141
                                               *****************************************************97..8*********** PP

                                 TIGR01930 138 dqllkdl..vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..k 202
                                               d+++  l  +    +mg+tAe +a+++gisRe+qD++al+S++++a+A+eeg+f+ +ivpve+  +  +
  lcl|NCBI__GCF_000015985.1:WP_043827862.1 142 DMMTGALncPFGTGHMGITAEIVAERHGISREDQDAFALESQTRTARAQEEGRFDGQIVPVEIASRkgP 210
                                               *88777799999***************************************************999999 PP

                                 TIGR01930 203 kvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivs 271
                                               +++s+De+++  ttle+La+L+paf++  g tvtAgN+s++nDGA+al+l+ e ++   g +pl+r+++
  lcl|NCBI__GCF_000015985.1:WP_043827862.1 211 VSFSRDEHPK-ATTLEALAGLRPAFQK-GG-TVTAGNASGINDGAGALILAREGAVP--GARPLGRLIG 274
                                               *********9.89************95.68.7*********************9886..788******* PP

                                 TIGR01930 272 aavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiA 340
                                               +a+agvdpe+mglgp+pA++++ +++gls+ d+d++E nEAFAaq+lav+++l+  d+++vN nGGAiA
  lcl|NCBI__GCF_000015985.1:WP_043827862.1 275 YAHAGVDPEVMGLGPIPAVQALCARTGLSVADFDVIESNEAFAAQALAVARALD-FDPARVNPNGGAIA 342
                                               ******************************************************.78************ PP

                                 TIGR01930 341 lGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               lGHP+Ga+Ga+i+++ l+eL++ g++++l+t+C+ggGqG+A+ le
  lcl|NCBI__GCF_000015985.1:WP_043827862.1 343 LGHPVGATGAIITVKALHELHRTGGRRALVTMCIGGGQGIALALE 387
                                               *****************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (389 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: 9.81
//
[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