Alignments for a candidate for fadA in Steroidobacter denitrificans DSM 18526

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Steroidobacter denitrificans DSM 18526

Align 3-ketoacyl-CoA thiolase [isoleucine degradation] (EC 2.3.1.16) (characterized)
to candidate WP_210399202.1 ACG33_RS06435 acetyl-CoA C-acyltransferase

Query= reanno::MR1:200842
         (396 letters)



>NCBI__GCF_001579945.1:WP_210399202.1
          Length = 392

 Score =  464 bits (1193), Expect = e-135
 Identities = 231/390 (59%), Positives = 292/390 (74%)

Query: 6   LNQEIVIVAAKRTPMGSFQGSLSGITSLSLAATAIKALLADTQVAPDKVDEVLMGCVLPA 65
           + ++I IVAA+RTP+GSFQG LS +++  L A A +A + D+ +   ++DE +MGCVL A
Sbjct: 1   MTEDIYIVAARRTPIGSFQGVLSSVSAPYLGAAAARAAIQDSGLDAGRIDEAIMGCVLMA 60

Query: 66  GLGQAPARQATLGAGLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSAKVVIAGGMESMS 125
           G+GQAPARQA L AG+P  V ATT+NK+CGS +K  MLA D I AGSA++V+AGG+ESM+
Sbjct: 61  GVGQAPARQAALAAGVPQKVPATTINKMCGSALKATMLAADQIAAGSARIVLAGGLESMT 120

Query: 126 QAPYLLDKARAGIRMGHGKVLDHMFLDGLEDAYTGGAMGTFAQKTADEFGITREQMDAFA 185
            APYLL KAR G+RMGHG++LDHMF DGL+ A+ G  MG FA  TA ++  TREQ D+FA
Sbjct: 121 NAPYLLPKARGGLRMGHGEILDHMFFDGLQSAFDGKPMGFFADATAKKYSFTREQQDSFA 180

Query: 186 LSSLEKANAAINSGAFKTEIVPVTVSDRRGDVTIDTDEQPGNARPEKIPTLRPAFAKDGT 245
             S+ +A AAI +G F+ EI PV + DR+G+ T+  DE P N   E+IP L+PAF KDGT
Sbjct: 181 AESVRRALAAIEAGRFEPEIAPVIIKDRKGERTVAKDETPFNCDIERIPQLKPAFNKDGT 240

Query: 246 ITAANSSSISDGAAALMLTTRANAEQLGLTVLATIKGHTTHAQEPALFTTAPVGAMAKLL 305
           +TAA+SSSISDGAAA+++   A   +  L  LA I GH ++AQ P  FTTAPVGA+  +L
Sbjct: 241 VTAASSSSISDGAAAVVIAGAAAVREHDLRPLARIVGHASYAQAPEWFTTAPVGAIQSVL 300

Query: 306 SNVGWSKDEVDLFEINEAFAMVTMLAVSELGLDMTKVNVNGGACALGHPIGCSGARLLVT 365
              GW   EVDL+EINEAFA VTM A+ +LGLD  +VNVNGGACALGHPIG +GAR+L T
Sbjct: 301 DKAGWRAAEVDLYEINEAFACVTMAAIHDLGLDHARVNVNGGACALGHPIGATGARILTT 360

Query: 366 LIHALKARGLKRGVASLCIGGGEATAMAIE 395
           LIH LK RG KRG+ASLCIGGGEA A+AIE
Sbjct: 361 LIHELKRRGQKRGIASLCIGGGEAAALAIE 390


Lambda     K      H
   0.316    0.131    0.364 

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: 461
Number of extensions: 9
Number of successful extensions: 1
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: 396
Length of database: 392
Length adjustment: 31
Effective length of query: 365
Effective length of database: 361
Effective search space:   131765
Effective search space used:   131765
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_210399202.1 ACG33_RS06435 (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.1906942.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.1e-131  422.2   7.1     1e-130  422.1   7.1    1.0  1  NCBI__GCF_001579945.1:WP_210399202.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001579945.1:WP_210399202.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.1   7.1    1e-130    1e-130       1     385 []       7     390 ..       7     390 .. 0.98

  Alignments for each domain:
  == domain 1  score: 422.1 bits;  conditional E-value: 1e-130
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 
                                           iv+a Rtpig+++g+l+++sa  L+aa+ +++++ +gld+ +ide+i+G+vl ag ++++aR+aalaag+p++
  NCBI__GCF_001579945.1:WP_210399202.1   7 IVAARRTPIGSFQGVLSSVSAPYLGAAAARAAIQDSGLDAGRIDEAIMGCVLMAGVGQAPARQAALAAGVPQK 79 
                                           89*********************************************************************** PP

                             TIGR01930  74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144
                                           vpa+t+n++C+S+l+A +laa++i+aG a++v+aGG+Esm+++p+ll+++  r +l++g+ +  d++  d+  
  NCBI__GCF_001579945.1:WP_210399202.1  80 VPATTINKMCGSALKATMLAADQIAAGSARIVLAGGLESMTNAPYLLPKA--RGGLRMGHGEILDHMFFDGlq 150
                                           ************************************************98..89***********99999999 PP

                             TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpn 214
                                            + ++ +mg  A+ +akky+++Re+qD++a++S ++a +Aie+g+f+ ei pv +k++  +++v+kDe++  n
  NCBI__GCF_001579945.1:WP_210399202.1 151 sAFDGKPMGFFADATAKKYSFTREQQDSFAAESVRRALAAIEAGRFEPEIAPVIIKDRkgERTVAKDETPF-N 222
                                           98899************************************************999999999999999987.9 PP

                             TIGR01930 215 ttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpv 287
                                             +e++ +Lkpaf++ +g tvtA++ss+++DGAaa++++  ++++e++l+plariv++a  +  pe ++++pv
  NCBI__GCF_001579945.1:WP_210399202.1 223 CDIERIPQLKPAFNK-DG-TVTAASSSSISDGAAAVVIAGAAAVREHDLRPLARIVGHASYAQAPEWFTTAPV 293
                                           *************95.9*.6***************************************************** PP

                             TIGR01930 288 pAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeL 360
                                            Ai+ +L+kag+++ ++dl+EinEAFA +++a++++lg ld+++vNvnGGA AlGHP+Ga+Gari++tl++eL
  NCBI__GCF_001579945.1:WP_210399202.1 294 GAIQSVLDKAGWRAAEVDLYEINEAFACVTMAAIHDLG-LDHARVNVNGGACALGHPIGATGARILTTLIHEL 365
                                           **************************************.89******************************** PP

                             TIGR01930 361 kergkkyGlatlCvggGqGaAvile 385
                                           k+rg+k+G+a+lC+ggG +aA+ +e
  NCBI__GCF_001579945.1:WP_210399202.1 366 KRRGQKRGIASLCIGGGEAAALAIE 390
                                           *********************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (392 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 26.54
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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