GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Nocardioides daejeonensis MJ31

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_110204929.1 DNK54_RS00015 acetyl-CoA C-acetyltransferase

Query= SwissProt::P14611
         (393 letters)



>NCBI__GCF_003194585.1:WP_110204929.1
          Length = 395

 Score =  354 bits (909), Expect = e-102
 Identities = 200/392 (51%), Positives = 256/392 (65%), Gaps = 4/392 (1%)

Query: 1   MTDVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAG 60
           M+  VIV+ ART VG+  G L  + A +LG V IK ALE+AG+  +QV  V+MG V+ AG
Sbjct: 1   MSGSVIVAGARTPVGRLLGGLKDLSAADLGGVAIKGALEKAGISGDQVDYVVMGHVIQAG 60

Query: 61  SGQNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMSA 120
           +GQ  ARQAA+K G+P  VP++TINKVC SG+ A+ LA   I AG+ EIVVAGG E+M+ 
Sbjct: 61  AGQITARQAAVKGGIPMGVPSLTINKVCLSGINAIALADQLIRAGEHEIVVAGGMESMTQ 120

Query: 121 APHVLPGSRDGFRMGDAKLVDTMIVDGLWDVYNQYHMGITAE--NVAKEYGITREAQDEF 178
           APH+LP SR+GF+ GD KLVD+M  D L+D +    MG   E  NVA    +TRE QD F
Sbjct: 121 APHLLPKSREGFKYGDTKLVDSMAYDALYDQFTDQAMGNLTEQCNVAGG-NLTREEQDAF 179

Query: 179 AVGSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLKPAFDK 238
           +  S   A AAQK G FD+EIVPV I  R+GD V    DE VR   T +S+ GL+PAF K
Sbjct: 180 SARSHQLAAAAQKNGVFDDEIVPVTISSRRGD-VVVSVDEGVRGDTTAESLGGLRPAFAK 238

Query: 239 AGTVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGPVPASK 298
            GT+TA ++S ++DGA AVVVMS AKA+ELGL  LA I +          + + P  A  
Sbjct: 239 DGTITAGSSSQISDGACAVVVMSKAKAEELGLEWLAEIGASGQVAGPDSTLQLQPARAIA 298

Query: 299 RALSRAEWTPQDLDLMEINEAFAAQALAVHQQMGWDTSKVNVNGGAIAIGHPIGASGCRI 358
           +A+ +      D+DL E+NEAFAA  +   +++G    KVNVNGGAIAIGHP+G SG RI
Sbjct: 299 KAVEKEGIAVSDIDLFELNEAFAAVGIESARELGVSEDKVNVNGGAIAIGHPVGMSGARI 358

Query: 359 LVTLLHEMKRRDAKKGLASLCIGGGMGVALAV 390
           ++ L  E+KRR    G A+LC GGG G AL V
Sbjct: 359 VLHLALELKRRGGGIGAAALCGGGGQGDALIV 390


Lambda     K      H
   0.315    0.131    0.369 

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: 451
Number of extensions: 16
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: 393
Length of database: 395
Length adjustment: 31
Effective length of query: 362
Effective length of database: 364
Effective search space:   131768
Effective search space used:   131768
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_110204929.1 DNK54_RS00015 (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.156848.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     6e-136  439.3   8.6   6.8e-136  439.1   8.6    1.0  1  NCBI__GCF_003194585.1:WP_110204929.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003194585.1:WP_110204929.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  439.1   8.6  6.8e-136  6.8e-136       1     384 [.       6     390 ..       6     391 .. 0.98

  Alignments for each domain:
  == domain 1  score: 439.1 bits;  conditional E-value: 6.8e-136
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 
                                           iv+++Rtp+g+l g lk+lsa+dL+  +ik++le+ag++ +++d+v++G+v+qag+++ +aR+aa++ g+p  
  NCBI__GCF_003194585.1:WP_110204929.1   6 IVAGARTPVGRLLGGLKDLSAADLGGVAIKGALEKAGISGDQVDYVVMGHVIQAGAGQITARQAAVKGGIPMG 78 
                                           8*********99************************************************************* PP

                             TIGR01930  74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144
                                           vp+lt+n+vC Sg++A+ala q i+aGe ++vvaGG+Esm+++p+ll++s  re++k+g++kl d++++d+  
  NCBI__GCF_003194585.1:WP_110204929.1  79 VPSLTINKVCLSGINAIALADQLIRAGEHEIVVAGGMESMTQAPHLLPKS--REGFKYGDTKLVDSMAYDAly 149
                                           ************************************************98..9*****************99* PP

                             TIGR01930 145 .vktklsmgetAenlakk.ygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirp 213
                                            + t+ +mg+ +e++     +++ReeqD++++rShq aa+A+++g f+deivpv++  +  ++vvs Deg+r 
  NCBI__GCF_003194585.1:WP_110204929.1 150 dQFTDQAMGNLTEQCNVAgGNLTREEQDAFSARSHQLAAAAQKNGVFDDEIVPVTISSRrgDVVVSVDEGVRG 222
                                           999**********88755268***********************************999999*********** PP

                             TIGR01930 214 nttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgp 286
                                           +tt+e+L++L+paf++ +g t+tAg+ssq++DGA+a+++ms+++a+elgl++la+i + ++++ + ++++l+p
  NCBI__GCF_003194585.1:WP_110204929.1 223 DTTAESLGGLRPAFAK-DG-TITAGSSSQISDGACAVVVMSKAKAEELGLEWLAEIGASGQVAGPDSTLQLQP 293
                                           **************95.9*.6**************************************************** PP

                             TIGR01930 287 vpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllke 359
                                           + Ai ka++k+g+ +sdidl+E+nEAFAa+ + +++elg  +++kvNvnGGAiA+GHP+G+sGarivl+l+ e
  NCBI__GCF_003194585.1:WP_110204929.1 294 ARAIAKAVEKEGIAVSDIDLFELNEAFAAVGIESARELG-VSEDKVNVNGGAIAIGHPVGMSGARIVLHLALE 365
                                           ***************************************.77******************************* PP

                             TIGR01930 360 LkergkkyGlatlCvggGqGaAvil 384
                                           Lk+rg+ +G a+lC ggGqG A+i+
  NCBI__GCF_003194585.1:WP_110204929.1 366 LKRRGGGIGAAALCGGGGQGDALIV 390
                                           ***********************98 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: 14.56
//
[ok]

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

Links

Downloads

Related tools

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