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 acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_013077129.1 BTUS_RS16115 acetyl-CoA C-acetyltransferase

Query= BRENDA::P45359
         (392 letters)



>NCBI__GCF_000092905.1:WP_013077129.1
          Length = 394

 Score =  523 bits (1347), Expect = e-153
 Identities = 260/391 (66%), Positives = 321/391 (82%), Gaps = 1/391 (0%)

Query: 1   MKEVVIASAVRTAIGSYGKSLKDVPAVDLGATAIKEAVKKAGIKPEDVNEVILGNVLQAG 60
           M +VVI SAVRTA+G++  +L  VPA +LGA  +KEA  + G+ PE ++EVI+GNVLQAG
Sbjct: 1   MVDVVITSAVRTAVGTFQGALSRVPAPELGAAVLKEAAARGGVDPERLDEVIMGNVLQAG 60

Query: 61  LGQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMSR 120
           LGQNPARQA+ KAG+P E+P+MTINKVCGSGL+ V LAAQ I+AGDA++++AGGMENMSR
Sbjct: 61  LGQNPARQAAMKAGIPQEVPSMTINKVCGSGLKAVMLAAQAIRAGDAEMLLAGGMENMSR 120

Query: 121 APYLANNARWGYRMGNAKFVDEMITDGLWDAFNDYHMGITAENIAERWNISREEQDEFAL 180
           APYL   AR G RMG+A+ VD MI DGLW AF D HMGITAEN+AER+ ++REEQD FAL
Sbjct: 121 APYLTEGARSGLRMGHAELVDSMIKDGLWCAFTDVHMGITAENVAERYGLTREEQDAFAL 180

Query: 181 ASQKKAEEAIKSGQFKDEIVPVVIKGRKGE-TVVDTDEHPRFGSTIEGLAKLKPAFKKDG 239
            SQ+++  AI  G+FKDEIVPV I+GRKGE +V DTDEHPR  +T E LAKL+PAFKKDG
Sbjct: 181 RSQRRSAAAIAEGRFKDEIVPVEIRGRKGEVSVFDTDEHPRPSTTAEALAKLRPAFKKDG 240

Query: 240 TVTAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGSAGVDPAIMGYGPFYATKAA 299
           TVTAGNASGLND AA L +MSA +A E G KPL ++VSY SAG+DPA+MG GP YAT+ A
Sbjct: 241 TVTAGNASGLNDGAAALAVMSAARATESGAKPLVRVVSYASAGLDPAVMGLGPIYATRKA 300

Query: 300 IEKAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGAIALGHPIGASGARILV 359
           +++AG T+ ++ L+E+NEAFAAQSLAVA++L      +NVNGGAIALGHPIGASGARILV
Sbjct: 301 LDRAGLTMADIGLVEANEAFAAQSLAVARELNIPDEILNVNGGAIALGHPIGASGARILV 360

Query: 360 TLVHAMQKRDAKKGLATLCIGGGQGTAILLE 390
           TL+H M++R  + GLATLCIGGGQG A+++E
Sbjct: 361 TLIHEMKRRGVRYGLATLCIGGGQGAAMIVE 391


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: 539
Number of extensions: 16
Number of successful extensions: 2
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: 394
Length adjustment: 31
Effective length of query: 361
Effective length of database: 363
Effective search space:   131043
Effective search space used:   131043
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_013077129.1 BTUS_RS16115 (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.6073.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-157  510.7   8.9   1.4e-157  510.5   8.9    1.0  1  lcl|NCBI__GCF_000092905.1:WP_013077129.1  BTUS_RS16115 acetyl-CoA C-acetyl


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092905.1:WP_013077129.1  BTUS_RS16115 acetyl-CoA C-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  510.5   8.9  1.4e-157  1.4e-157       1     385 []       6     391 ..       6     391 .. 0.99

  Alignments for each domain:
  == domain 1  score: 510.5 bits;  conditional E-value: 1.4e-157
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 
                                               i +avRt++g+++g+l+ ++a +L+aav+ke+ +r g+dpe++devi+Gnvlqag ++n+aR+aa++ag
  lcl|NCBI__GCF_000092905.1:WP_013077129.1   6 ITSAVRTAVGTFQGALSRVPAPELGAAVLKEAAARGGVDPERLDEVIMGNVLQAGLGQNPARQAAMKAG 74 
                                               779****************************************************************** PP

                                 TIGR01930  70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138
                                               +p++vp++t+n+vC+Sgl+Av+laaq+i+aG+a++++aGG+E+mSr+p+l++ +  r++l++g+a+l d
  lcl|NCBI__GCF_000092905.1:WP_013077129.1  75 IPQEVPSMTINKVCGSGLKAVMLAAQAIRAGDAEMLLAGGMENMSRAPYLTEGA--RSGLRMGHAELVD 141
                                               *************************************************99997..89*********** PP

                                 TIGR01930 139 qllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk... 201
                                               +++kd+   + t+++mg+tAen+a++yg++ReeqD++alrS++++a+Ai+eg+fkdeivpve++g+   
  lcl|NCBI__GCF_000092905.1:WP_013077129.1 142 SMIKDGlwcAFTDVHMGITAENVAERYGLTREEQDAFALRSQRRSAAAIAEGRFKDEIVPVEIRGRkge 210
                                               *********99******************************************************9999 PP

                                 TIGR01930 202 kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplariv 270
                                                 v+++De++rp tt+e+LakL+pafk+ +g tvtAgN+s+lnDGAaal +ms ++a e g +pl r+v
  lcl|NCBI__GCF_000092905.1:WP_013077129.1 211 VSVFDTDEHPRPSTTAEALAKLRPAFKK-DG-TVTAGNASGLNDGAAALAVMSAARATESGAKPLVRVV 277
                                               999***********************95.9*.6************************************ PP

                                 TIGR01930 271 saavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAi 339
                                               s+a ag+dp++mglgp++A++kaL++agl++ di lvE nEAFAaq lav++el+ + +e +NvnGGAi
  lcl|NCBI__GCF_000092905.1:WP_013077129.1 278 SYASAGLDPAVMGLGPIYATRKALDRAGLTMADIGLVEANEAFAAQSLAVARELN-IPDEILNVNGGAI 345
                                               *******************************************************.889********** PP

                                 TIGR01930 340 AlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               AlGHP+GasGari++tl++e+k+rg++yGlatlC+ggGqGaA+i+e
  lcl|NCBI__GCF_000092905.1:WP_013077129.1 346 ALGHPIGASGARILVTLIHEMKRRGVRYGLATLCIGGGQGAAMIVE 391
                                               ********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (394 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: 7.82
//
[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