GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Kocuria flava HO-9041

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_058860019.1 AS188_RS15780 acetyl-CoA C-acyltransferase

Query= metacyc::MONOMER-3207
         (400 letters)



>NCBI__GCF_001482365.1:WP_058860019.1
          Length = 399

 Score =  399 bits (1025), Expect = e-116
 Identities = 212/402 (52%), Positives = 284/402 (70%), Gaps = 5/402 (1%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           M + F+    RTP+GR+GGAL+ VR DDLAA+ +K  +  +  +    VDEV  G AN A
Sbjct: 1   MTEAFLVGGARTPVGRYGGALSSVRPDDLAALVVKHAVT-DAGIDPHDVDEVILGNANGA 59

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           GE+NRNVARMA LLAG P+++PG+T+NRLCAS + AI  A   I +G  ++ +AGGVESM
Sbjct: 60  GEENRNVARMAWLLAGFPDTVPGITVNRLCASSLSAIIMASHMIKAGAADVVVAGGVESM 119

Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVD-SMPETADNVADDYQVSRA 179
           SRAP+VM K  + +++  ++ DT+IGWRF NP  K    +  SMPETA+ VA    ++R 
Sbjct: 120 SRAPWVMEKPATAFAKPGEVFDTSIGWRFTNPEFKKHDKMTYSMPETAEEVAAVDGITRE 179

Query: 180 DQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKG-ETIVERDEHLRPETTLEALTKLK 238
           D DAFA+ S +KA AA  AG FA+EIVPV +  +KG ET+V+ DE  RP TT++ L KL+
Sbjct: 180 DADAFAVASHEKAIAAIDAGRFADEIVPVTVKGRKGAETVVDTDEGPRPGTTMDVLAKLR 239

Query: 239 PVNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGP 298
           PV      VTAGN+S +NDGA+A+++ S  A +K+GLT RAR++  AS GVAP +MG+GP
Sbjct: 240 PVVTHGSVVTAGNSSSLNDGASAILVVSERAAEKYGLTARARIVDGASAGVAPEIMGLGP 299

Query: 299 VPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPL 358
           VPA +K+ ER G  + D   +ELNEAFASQ LA +R LG+  D   VN +GGAIALGH L
Sbjct: 300 VPATQKVLERTGWGIGDLGAVELNEAFASQSLACIRRLGL--DEGIVNNDGGAIALGHAL 357

Query: 359 GMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           G SG+RLV+T L ++E+ G  +GLATMCVGVGQG A+ +E++
Sbjct: 358 GSSGSRLVVTLLGRMEREGAERGLATMCVGVGQGTAMLVEKI 399


Lambda     K      H
   0.318    0.134    0.383 

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: 445
Number of extensions: 21
Number of successful extensions: 5
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: 400
Length of database: 399
Length adjustment: 31
Effective length of query: 369
Effective length of database: 368
Effective search space:   135792
Effective search space used:   135792
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_058860019.1 AS188_RS15780 (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.2980870.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.3e-142  459.2   3.0     6e-142  459.0   3.0    1.0  1  NCBI__GCF_001482365.1:WP_058860019.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001482365.1:WP_058860019.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  459.0   3.0    6e-142    6e-142       2     385 .]       7     397 ..       6     397 .. 0.97

  Alignments for each domain:
  == domain 1  score: 459.0 bits;  conditional E-value: 6e-142
                             TIGR01930   2 vdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaaglpes 73 
                                           v+++Rtp+g++gg+l++++++dL+a v+k+++  ag+dp+++devilGn+  age+  n+aR+a l ag+p++
  NCBI__GCF_001482365.1:WP_058860019.1   7 VGGARTPVGRYGGALSSVRPDDLAALVVKHAVTDAGIDPHDVDEVILGNANGAGEEnRNVARMAWLLAGFPDT 79 
                                           89*******99*********************************************9**************** PP

                             TIGR01930  74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144
                                           vp++tvnr+CaS+l A+++a ++ikaG+advvvaGGvEsmSr+p+++++  +++ +k+g+  + +   + +  
  NCBI__GCF_001482365.1:WP_058860019.1  80 VPGITVNRLCASSLSAIIMASHMIKAGAADVVVAGGVESMSRAPWVMEKP-ATAFAKPGEVFDTSIGWR-Ftn 150
                                           *********************************************99997.788888877766663333.258 PP

                             TIGR01930 145 ......vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...kkvvskD 208
                                                 +k  +sm etAe++a+  gi+Re+ D++a++Sh+ka +Ai++g+f+deivpv+vkg+   ++vv++D
  NCBI__GCF_001482365.1:WP_058860019.1 151 pefkkhDKMTYSMPETAEEVAAVDGITREDADAFAVASHEKAIAAIDAGRFADEIVPVTVKGRkgaETVVDTD 223
                                           899999999*****************************************************9**999***** PP

                             TIGR01930 209 egirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpee 281
                                           eg+rp+tt++ LakL+p+ +  +gs+vtAgNss+lnDGA+a+l++se++a+++glt  ariv+ a agv pe+
  NCBI__GCF_001482365.1:WP_058860019.1 224 EGPRPGTTMDVLAKLRPVVT--HGSVVTAGNSSSLNDGASAILVVSERAAEKYGLTARARIVDGASAGVAPEI 294
                                           *******************7..799************************************************ PP

                             TIGR01930 282 mglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivl 354
                                           mglgpvpA++k+L+++g+ i d+ +vE+nEAFA+q la+++ lg ld+  vN  GGAiAlGH lG+sG+r+v+
  NCBI__GCF_001482365.1:WP_058860019.1 295 MGLGPVPATQKVLERTGWGIGDLGAVELNEAFASQSLACIRRLG-LDEGIVNNDGGAIALGHALGSSGSRLVV 366
                                           ********************************************.88************************** PP

                             TIGR01930 355 tllkeLkergkkyGlatlCvggGqGaAvile 385
                                           tll +++++g+++Glat+Cvg GqG+A+++e
  NCBI__GCF_001482365.1:WP_058860019.1 367 TLLGRMEREGAERGLATMCVGVGQGTAMLVE 397
                                           ****************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (399 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 26.28
//
[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:

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:

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:

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:

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