Alignments for a candidate for fadA in Kyrpidia tusciae DSM 2912

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Kyrpidia tusciae DSM 2912

Align 3-oxo-acyl CoA thiolase (EC 2.3.1.16) (characterized)
to candidate WP_013074586.1 BTUS_RS02645 thiolase family protein

Query= metacyc::G185E-7833-MONOMER
         (386 letters)



>NCBI__GCF_000092905.1:WP_013074586.1
          Length = 395

 Score =  361 bits (927), Expect = e-104
 Identities = 196/395 (49%), Positives = 261/395 (66%), Gaps = 11/395 (2%)

Query: 1   MTEAYVIDAVRTAVGKRGGALAGIHPVDLGALAWRGLLDRTDIDPAAVDDVIAGCVDAIG 60
           M EA ++DA+RT +G+R G+LA +HPVDL A   + L+ R+ +D A VDDVI GCVD +G
Sbjct: 1   MREAVIVDAIRTPIGRRRGSLAQVHPVDLLAGVLKELIRRSGLDAAVVDDVIVGCVDQVG 60

Query: 61  GQAGNIARLSWLAAGYPEEVPGVTVDRQCGSSQQAISFGAQAIMSGTADVIVAGGVQNMS 120
            Q+ NI R +WL+AG PE VP VT+DRQCGSS QA+ F AQ +M+G  D+ +A GV++M+
Sbjct: 61  EQSVNIGRNAWLSAGLPESVPAVTIDRQCGSSLQALHFAAQGVMAGVYDIAIAAGVESMT 120

Query: 121 QIPISSAMTVGEQFGFTSPTNESKQWLHRYGDQEISQFRGSELIAEKWNLSREEMERYSL 180
           ++P+ S  T+G      +   + +  + R+  Q   Q  G+E+IA++W  +RE+++R+ L
Sbjct: 121 RVPMMS--TIGVHGVPMTRDLQERYRMDRWNRQFFDQALGAEMIAKQWGFTREDLDRFGL 178

Query: 181 TSHERAFAAIRAGHFENEIITVET-------ESGPFRVDEGPR-ESSLEKMAGLQPLVEG 232
            SHE A  A + G F  EI+ V+        E   F  DEG R ++SLEKM  L P  E 
Sbjct: 179 RSHELATKARQKGCFAREIVPVQVPVPDAPGEYRTFAEDEGIRPDTSLEKMLALPPAFED 238

Query: 233 GRL-TAAMASQISDGASAVLLASERAVKDHGLRPRARIHHISARAADPVFMLTGPIPATR 291
             L TA  ASQISDGASA L+ S    +  GLRPRAR    +A   DPV MLTGPIPAT+
Sbjct: 239 LELITAGNASQISDGASAALVMSRETAERLGLRPRARFVAFAAVGVDPVTMLTGPIPATQ 298

Query: 292 YALDKTGLAIDDIDTVEINEAFAPVVMAWLKEIKADPAKVNPNGGAIALGHPLGATGAKL 351
             L++ GL ++DID  E+NEAFA VV+AW KEI A   KVN +GGA+A+GHPLGATG ++
Sbjct: 299 KVLERAGLKVEDIDLFEVNEAFASVVLAWQKEIGAPWDKVNVHGGAVAIGHPLGATGTRI 358

Query: 352 FTTMLGELERIGGRYGLQTMCEGGGTANVTIIERL 386
             T+L  LE   GRYGL  +CEGGG AN TIIER+
Sbjct: 359 TATLLNGLEERKGRYGLMAICEGGGMANATIIERI 393


Lambda     K      H
   0.317    0.134    0.389 

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: 403
Number of extensions: 14
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: 386
Length of database: 395
Length adjustment: 31
Effective length of query: 355
Effective length of database: 364
Effective search space:   129220
Effective search space used:   129220
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_013074586.1 BTUS_RS02645 (thiolase family protein)
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.11971.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.7e-147  475.1   0.0   8.7e-147  475.0   0.0    1.0  1  lcl|NCBI__GCF_000092905.1:WP_013074586.1  BTUS_RS02645 thiolase family pro


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092905.1:WP_013074586.1  BTUS_RS02645 thiolase family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  475.0   0.0  8.7e-147  8.7e-147       1     385 []       6     391 ..       6     391 .. 0.97

  Alignments for each domain:
  == domain 1  score: 475.0 bits;  conditional E-value: 8.7e-147
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaa 68 
                                               ivda+Rtpig+ +gsl++++++dLla v+kel++r+gld++ +d+vi+G+v q geq +ni+R+a l+a
  lcl|NCBI__GCF_000092905.1:WP_013074586.1   6 IVDAIRTPIGRRRGSLAQVHPVDLLAGVLKELIRRSGLDAAVVDDVIVGCVDQVGEQsVNIGRNAWLSA 74 
                                               9*********88********************************************************* PP

                                 TIGR01930  69 glpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakle 137
                                               glpesvpa+t++r+C+S+lqA++ aaq ++aG +d+++a+GvEsm+rvp+++      +++ + +  +e
  lcl|NCBI__GCF_000092905.1:WP_013074586.1  75 GLPESVPAVTIDRQCGSSLQALHFAAQGVMAGVYDIAIAAGVESMTRVPMMSTIG--VHGVPMTRDLQE 141
                                               *************************************************988876..667777666666 PP

                                 TIGR01930 138 dqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..... 201
                                                 +++  +++ + ++  Ae++ak++g++Re++D++ lrSh+ a+kA ++g f++eivpv+v+       
  lcl|NCBI__GCF_000092905.1:WP_013074586.1 142 RYRMDRWNRQFFDQALGAEMIAKQWGFTREDLDRFGLRSHELATKARQKGCFAREIVPVQVPVPdapge 210
                                               667777899****************************************************99999999 PP

                                 TIGR01930 202 kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplariv 270
                                                +++++Degirp+t+lek+  L+paf++   + +tAgN+sq++DGA+a+l+ms+e+a++lgl+p ar+v
  lcl|NCBI__GCF_000092905.1:WP_013074586.1 211 YRTFAEDEGIRPDTSLEKMLALPPAFED--LELITAGNASQISDGASAALVMSRETAERLGLRPRARFV 277
                                               99************************85..667************************************ PP

                                 TIGR01930 271 saavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAi 339
                                               ++a +gvdp +m++gp+pA++k+L++agl+++didl+E+nEAFA++vla++ke+g    +kvNv+GGA+
  lcl|NCBI__GCF_000092905.1:WP_013074586.1 278 AFAAVGVDPVTMLTGPIPATQKVLERAGLKVEDIDLFEVNEAFASVVLAWQKEIG-APWDKVNVHGGAV 345
                                               *******************************************************.779********** PP

                                 TIGR01930 340 AlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               A+GHPlGa+G+ri++tll+ L+er+++yGl+++C ggG+++A+i+e
  lcl|NCBI__GCF_000092905.1:WP_013074586.1 346 AIGHPLGATGTRITATLLNGLEERKGRYGLMAICEGGGMANATIIE 391
                                               ********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (395 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: 10.30
//
[ok]

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

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Steps (tab-delimited)
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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