Alignments for a candidate for fadA in Desulfacinum infernum DSM 9756

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Desulfacinum infernum DSM 9756

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_073041860.1 BUB04_RS17410 acetyl-CoA C-acetyltransferase

Query= BRENDA::P45359
         (392 letters)



>NCBI__GCF_900129305.1:WP_073041860.1
          Length = 400

 Score =  399 bits (1025), Expect = e-116
 Identities = 213/395 (53%), Positives = 276/395 (69%), Gaps = 5/395 (1%)

Query: 2   KEVVIASAVRTAIGSYGKSLKDVPAVDLGATAIKEAVKKAGIK-PEDVNEVILGNVLQAG 60
           ++VVI SA RT IG +G SLKDV A  L A  +KE +K+AG   P  ++EV+ G+  Q  
Sbjct: 5   RDVVIVSAARTPIGKFGGSLKDVRASSLLALVMKEVLKRAGNPDPSILDEVVTGDCAQCF 64

Query: 61  LGQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMSR 120
              N AR A  KAGLPVEIPA TI + C S ++ ++ A Q+IKAGDADV++ GG+E+MS 
Sbjct: 65  DEANTARTAMLKAGLPVEIPAHTIQRQCASSMQALAAATQMIKAGDADVVLVGGVESMSS 124

Query: 121 APYLANNARWGYRMGNAKFVD---EMITDGLWDAFNDYHMGITAENIAERWNISREEQDE 177
           APY   NARWG R+ N + VD   EM+  G     N   MG TAEN+AE++ ISR+EQDE
Sbjct: 125 APYYLPNARWGMRLMNHEVVDSVWEMLHSGSRLLGNPMIMGQTAENLAEKYGISRQEQDE 184

Query: 178 FALASQKKAEEAIKSGQFKDEIVPVVIKGRKGETVV-DTDEHPRFGSTIEGLAKLKPAFK 236
            AL S   AE AIK G+FKD+IVPV I G KG+T V + DEHPRFG T++ LAKLKP FK
Sbjct: 185 VALRSHHNAETAIKEGRFKDQIVPVEIPGPKGKTAVFEQDEHPRFGLTMDDLAKLKPVFK 244

Query: 237 KDGTVTAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGSAGVDPAIMGYGPFYAT 296
           KDGTVTAGN+SGLND AA  ++M+  KAKE+G++PLA+IV+  +AGV+P  MGYGP  AT
Sbjct: 245 KDGTVTAGNSSGLNDGAAAALVMTRAKAKEMGLEPLARIVATAAAGVEPEYMGYGPVPAT 304

Query: 297 KAAIEKAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGAIALGHPIGASGAR 356
              ++KAG T+ ++ LIE NEAFAAQ +A  + + FD    NVNG  I LGHP+G +G R
Sbjct: 305 DKVLKKAGMTLKDIQLIELNEAFAAQYIACERGIGFDRAIANVNGSGIGLGHPVGCTGLR 364

Query: 357 ILVTLVHAMQKRDAKKGLATLCIGGGQGTAILLEK 391
           I+++L + M +RD   GLATLC+GGG G A ++ +
Sbjct: 365 IVISLAYEMARRDLSIGLATLCVGGGMGMATIVAR 399


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: 480
Number of extensions: 20
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: 400
Length adjustment: 31
Effective length of query: 361
Effective length of database: 369
Effective search space:   133209
Effective search space used:   133209
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_073041860.1 BUB04_RS17410 (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.31904.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     3e-147  476.5   2.3   3.4e-147  476.3   2.3    1.0  1  lcl|NCBI__GCF_900129305.1:WP_073041860.1  BUB04_RS17410 acetyl-CoA C-acety


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900129305.1:WP_073041860.1  BUB04_RS17410 acetyl-CoA C-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  476.3   2.3  3.4e-147  3.4e-147       1     384 [.       9     397 ..       9     398 .. 0.98

  Alignments for each domain:
  == domain 1  score: 476.3 bits;  conditional E-value: 3.4e-147
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageqaniaReaalaa 68 
                                               iv+a+Rtpigk+ggslk+++a++Lla v+ke+l+ra + dp+ +dev++G   q  ++an+aR+a+l+a
  lcl|NCBI__GCF_900129305.1:WP_073041860.1   9 IVSAARTPIGKFGGSLKDVRASSLLALVMKEVLKRAgNPDPSILDEVVTGDCAQCFDEANTARTAMLKA 77 
                                               8***********************************9******************************** PP

                                 TIGR01930  69 glpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakle 137
                                               glp ++pa+t++r+CaS++qA+a a q+ikaG+advv++GGvEsmS++p++l+++  r++++l + ++ 
  lcl|NCBI__GCF_900129305.1:WP_073041860.1  78 GLPVEIPAHTIQRQCASSMQALAAATQMIKAGDADVVLVGGVESMSSAPYYLPNA--RWGMRLMNHEVV 144
                                               ******************************************************8..899999999999 PP

                                 TIGR01930 138 dqllkdl......vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkg 200
                                               d++ + l        + + mg+tAenla+kygisR+eqDe alrSh++a++Ai+eg+fkd+ivpve++g
  lcl|NCBI__GCF_900129305.1:WP_073041860.1 145 DSVWEMLhsgsrlLGNPMIMGQTAENLAEKYGISRQEQDEVALRSHHNAETAIKEGRFKDQIVPVEIPG 213
                                               9888877899*998889***************************************************9 PP

                                 TIGR01930 201 k...kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltpl 266
                                                   + v+++De++r ++t+++LakLkp+fk+ +g tvtAgNss+lnDGAaa+l+m++++ake+gl+pl
  lcl|NCBI__GCF_900129305.1:WP_073041860.1 214 PkgkTAVFEQDEHPRFGLTMDDLAKLKPVFKK-DG-TVTAGNSSGLNDGAAAALVMTRAKAKEMGLEPL 280
                                               999999************************95.9*.6******************************** PP

                                 TIGR01930 267 arivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvn 335
                                               ariv++a agv+pe+mg+gpvpA+ k+Lkkag++++di+l+E+nEAFAaq++a+e+ +g  d++  Nvn
  lcl|NCBI__GCF_900129305.1:WP_073041860.1 281 ARIVATAAAGVEPEYMGYGPVPATDKVLKKAGMTLKDIQLIELNEAFAAQYIACERGIG-FDRAIANVN 348
                                               ***********************************************************.779****** PP

                                 TIGR01930 336 GGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvil 384
                                               G+ i lGHP+G++G riv++l++e+++r+  +GlatlCvggG+G+A+i+
  lcl|NCBI__GCF_900129305.1:WP_073041860.1 349 GSGIGLGHPVGCTGLRIVISLAYEMARRDLSIGLATLCVGGGMGMATIV 397
                                               ***********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (400 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.57
//
[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