Alignments for a candidate for fadA in Desulfatibacillum aliphaticivorans DSM 15576

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Desulfatibacillum aliphaticivorans DSM 15576

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_028314019.1 G491_RS0106655 acetyl-CoA C-acetyltransferase

Query= BRENDA::P45359
         (392 letters)



>NCBI__GCF_000429905.1:WP_028314019.1
          Length = 428

 Score =  402 bits (1033), Expect = e-116
 Identities = 211/429 (49%), Positives = 283/429 (65%), Gaps = 39/429 (9%)

Query: 1   MKEVVIASAVRTAIGSYGKSLKDVPAVDLGATAIKEAVKKAGIKP--------------- 45
           MKE VI S  RTAIGS+G  LK VP + LG+T +KE +K+  ++P               
Sbjct: 1   MKEAVIVSGARTAIGSFGGVLKSVPVIQLGSTVMKETLKRVNLRPVVSEAMLSAAPDALK 60

Query: 46  --------------ED------VNEVILGNVLQAGLGQNPARQASFKAGLPVEIPAMTIN 85
                         +D      ++EVI+GNVL +G GQNPARQA  +AG+  E PA T+N
Sbjct: 61  DQGVIELEEKGMDWDDSAQPVAIDEVIMGNVLTSGQGQNPARQAMVQAGICKETPAFTVN 120

Query: 86  KVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMSRAPYLANNARWGYRM---GNAKFVDE 142
           KVC SGL+ ++L A  I  G ADVI+AGG E+MS  P     ARWGYRM   G  +  D 
Sbjct: 121 KVCASGLKAIALGAASIMTGQADVILAGGQESMSNVPMALPLARWGYRMAISGKGEIDDL 180

Query: 143 MITDGLWDAFNDYHMGITAENIAERWNISREEQDEFALASQKKAEEAIKSGQFKDEIVPV 202
           M+ DGL++ F  YHMG+TAENIA ++ I+REEQD   + S  +A +AI  G FKDEIVPV
Sbjct: 181 MVLDGLYEIFYGYHMGVTAENIASKYGITREEQDALGVLSHNRARKAITEGLFKDEIVPV 240

Query: 203 VIKGRKGETVVDTDEHPRFGSTIEGLAKLKPAFKKDGTVTAGNASGLNDCAAVLVIMSAE 262
               R+ E VVDTDE P   +++E +AKL+PAF KDGTVTAGNASG+ND AA +++MSAE
Sbjct: 241 SFMERRKEVVVDTDERP-MDTSMEKMAKLRPAFIKDGTVTAGNASGINDGAASVLLMSAE 299

Query: 263 KAKELGVKPLAKIVSYGSAGVDPAIMGYGPFYATKAAIEKAGWTVDELDLIESNEAFAAQ 322
           KA+ELG++PLAKI ++ SAG+DPA MG GP  A +  ++  G ++D+L ++E NEAFA+Q
Sbjct: 300 KAQELGLEPLAKIKAFASAGMDPAYMGLGPIPAVRKVLKATGMSIDDLQMLEVNEAFASQ 359

Query: 323 SLAVAKDLKFDMNKVNVNGGAIALGHPIGASGARILVTLVHAMQKRDAKKGLATLCIGGG 382
           ++A  ++L  D  K N  G  I+LGHPIG +GAR +VT +H M+++    GL T+CIGGG
Sbjct: 360 AIACLRELGIDTEKPNELGSGISLGHPIGCTGARQMVTAIHHMERKGYNTGLITMCIGGG 419

Query: 383 QGTAILLEK 391
            G A+++EK
Sbjct: 420 MGMAMIIEK 428


Lambda     K      H
   0.315    0.132    0.375 

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: 520
Number of extensions: 27
Number of successful extensions: 4
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: 392
Length of database: 428
Length adjustment: 31
Effective length of query: 361
Effective length of database: 397
Effective search space:   143317
Effective search space used:   143317
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 WP_028314019.1 G491_RS0106655 (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.3798813.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-139  450.5   5.8   1.8e-132  427.9   3.8    2.0  2  NCBI__GCF_000429905.1:WP_028314019.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000429905.1:WP_028314019.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   1.9e-09   1.9e-09       1      44 [.       6      48 ..       6      65 .. 0.88
   2 !  427.9   3.8  1.8e-132  1.8e-132      39     385 .]      79     427 ..      71     427 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.9e-09
                             TIGR01930  1 ivdavRtpigklggslkelsaedLlaavikelleragldpekid 44
                                          iv+++Rt+ig++gg+lk+++  +L+++v+ke l+r++l p  + 
  NCBI__GCF_000429905.1:WP_028314019.1  6 IVSGARTAIGSFGGVLKSVPVIQLGSTVMKETLKRVNLRP-VVS 48
                                          8************************************998.444 PP

  == domain 2  score: 427.9 bits;  conditional E-value: 1.8e-132
                             TIGR01930  39 dpekidevilGnvlqageqaniaReaalaaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvE 111
                                           +p +idevi+Gnvl++g+++n+aR+a+++ag+ +++pa+tvn+vCaSgl+A+al+a++i++G+adv++aGG E
  NCBI__GCF_000429905.1:WP_028314019.1  79 QPVAIDEVIMGNVLTSGQGQNPARQAMVQAGICKETPAFTVNKVCASGLKAIALGAASIMTGQADVILAGGQE 151
                                           6889********************************************************************* PP

                             TIGR01930 112 smSrvpillkaslr.reslklgkakledqllkdl...vktklsmgetAenlakkygisReeqDeyalrShqka 180
                                           smS+vp+ l+ +++ ++++  gk + +d ++ d+      +++mg+tAen+a kygi+ReeqD++ + Sh++a
  NCBI__GCF_000429905.1:WP_028314019.1 152 SMSNVPMALPLARWgYRMAISGKGEIDDLMVLDGlyeIFYGYHMGVTAENIASKYGITREEQDALGVLSHNRA 224
                                           **********985434444445666677666666999889********************************* PP

                             TIGR01930 181 akAieegkfkdeivpvevkgk..kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaall 251
                                            kAi eg fkdeivpv++ ++  ++vv++De +  +t++ek+akL+paf + +g tvtAgN+s++nDGAa +l
  NCBI__GCF_000429905.1:WP_028314019.1 225 RKAITEGLFKDEIVPVSFMERrkEVVVDTDERPM-DTSMEKMAKLRPAFIK-DG-TVTAGNASGINDGAASVL 294
                                           *******************999777777777766.9*************95.9*.6***************** PP

                             TIGR01930 252 lmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekel 324
                                           lms e+a+elgl+pla+i ++a ag+dp++mglgp+pA++k+Lk +g+si+d+++ E+nEAFA+q++a+ +el
  NCBI__GCF_000429905.1:WP_028314019.1 295 LMSAEKAQELGLEPLAKIKAFASAGMDPAYMGLGPIPAVRKVLKATGMSIDDLQMLEVNEAFASQAIACLREL 367
                                           ************************************************************************* PP

                             TIGR01930 325 gsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                           g +d+ek N  G+ i+lGHP+G++Gar ++t +++++++g + Gl+t+C+ggG+G+A+i+e
  NCBI__GCF_000429905.1:WP_028314019.1 368 G-IDTEKPNELGSGISLGHPIGCTGARQMVTAIHHMERKGYNTGLITMCIGGGMGMAMIIE 427
                                           *.88*******************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (428 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: 00:00:00.00
# Mc/sec: 30.20
//
[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