GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Derxia gummosa DSM 723

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_028311754.1 H566_RS0112785 3-oxoadipyl-CoA thiolase

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



>NCBI__GCF_000482785.1:WP_028311754.1
          Length = 401

 Score =  545 bits (1405), Expect = e-160
 Identities = 270/401 (67%), Positives = 323/401 (80%), Gaps = 1/401 (0%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           M   ++CDAIRTP GR+GG+L+GVRADDL AVP++AL+  NP+V W  +D+V +GCANQA
Sbjct: 1   MTHAYLCDAIRTPFGRYGGSLSGVRADDLGAVPIRALMARNPSVDWAALDDVIYGCANQA 60

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           GEDNRNV RM+ LLAGLP  +PG T+NRLC S +DA  +A RAI +GE++L IAGGVESM
Sbjct: 61  GEDNRNVGRMSALLAGLPPEVPGTTVNRLCGSSLDATASAARAIRAGEVQLVIAGGVESM 120

Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180
           SRAPFVMGKA   +SR+ K+EDTTIGWRF+NPLMK+ +GVDSMPETA+NVA D+ V+RAD
Sbjct: 121 SRAPFVMGKATEAFSRSAKVEDTTIGWRFVNPLMKAMHGVDSMPETAENVATDFDVARAD 180

Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGET-IVERDEHLRPETTLEALTKLKP 239
           QDAFALRSQQ+AAAAQAAG  ++EI PV IA K+G+  +V  DEHLRPETTL AL KLK 
Sbjct: 181 QDAFALRSQQRAAAAQAAGRLSQEITPVTIAQKRGDALVVSADEHLRPETTLAALAKLKG 240

Query: 240 VNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPV 299
           V  PD TVTAGNASGVNDGAAAL+LAS     +HGL PRAR++  A  GVAPR+MG GP 
Sbjct: 241 VVRPDGTVTAGNASGVNDGAAALLLASEAGAARHGLKPRARIVASAVAGVAPRIMGFGPA 300

Query: 300 PAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLG 359
           PA+ K+     + +   DVIELNEAFA+Q LAV R  G+ADD  +VNPNGGAIALGHPLG
Sbjct: 301 PAITKVLALAKLRLDQIDVIELNEAFAAQALAVTRAHGLADDDARVNPNGGAIALGHPLG 360

Query: 360 MSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
            SGARLV+ ALH+LE++GGR GL TMC+GVGQG+AL IERV
Sbjct: 361 ASGARLVIAALHELERTGGRYGLCTMCIGVGQGIALVIERV 401


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: 513
Number of extensions: 14
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: 400
Length of database: 401
Length adjustment: 31
Effective length of query: 369
Effective length of database: 370
Effective search space:   136530
Effective search space used:   136530
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_028311754.1 H566_RS0112785 (3-oxoadipyl-CoA thiolase)
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.1609838.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.8e-139  448.8   6.9   8.8e-139  448.6   6.9    1.0  1  NCBI__GCF_000482785.1:WP_028311754.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000482785.1:WP_028311754.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  448.6   6.9  8.8e-139  8.8e-139       2     385 .]       7     399 ..       6     399 .. 0.95

  Alignments for each domain:
  == domain 1  score: 448.6 bits;  conditional E-value: 8.8e-139
                             TIGR01930   2 vdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaalaaglpe 72 
                                            da+Rtp+g++ggsl+ ++a+dL+a  i++l++r+  +d +++d+vi+G++ qage+  n++R+ al aglp 
  NCBI__GCF_000482785.1:WP_028311754.1   7 CDAIRTPFGRYGGSLSGVRADDLGAVPIRALMARNpSVDWAALDDVIYGCANQAGEDnRNVGRMSALLAGLPP 79 
                                           589******99**********************************************9*************** PP

                             TIGR01930  73 svpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl. 144
                                           +vp++tvnr+C+S+l+A a+aa++i+aGe ++v+aGGvEsmSr+p+++ +++  e ++ ++ak+ed+++    
  NCBI__GCF_000482785.1:WP_028311754.1  80 EVPGTTVNRLCGSSLDATASAARAIRAGEVQLVIAGGVESMSRAPFVMGKAT--EAFS-RSAKVEDTTIGWRf 149
                                           **********************************************999973..3333.45566663333326 PP

                             TIGR01930 145 .......vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...kkvvsk 207
                                                   +   sm etAen+a+++++ R +qD++alrS+q+aa+A+++g++++ei+pv++ +k   + vvs 
  NCBI__GCF_000482785.1:WP_028311754.1 150 vnplmkaMHGVDSMPETAENVATDFDVARADQDAFALRSQQRAAAAQAAGRLSQEITPVTIAQKrgdALVVSA 222
                                           7888997667789*************************************************999*9999*** PP

                             TIGR01930 208 DegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpe 280
                                           De++rp+ttl++LakLk + + ++g tvtAgN+s++nDGAaalll+se+ a+++gl+p ariv+ avagv p+
  NCBI__GCF_000482785.1:WP_028311754.1 223 DEHLRPETTLAALAKLKGVVR-PDG-TVTAGNASGVNDGAAALLLASEAGAARHGLKPRARIVASAVAGVAPR 293
                                           ********************9.69*.6********************************************** PP

                             TIGR01930 281 emglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsld.lekvNvnGGAiAlGHPlGasGari 352
                                           +mg+gp+pAi+k+L+ a+l++++id++E+nEAFAaq+lav+++ g+ d +++vN nGGAiAlGHPlGasGar+
  NCBI__GCF_000482785.1:WP_028311754.1 294 IMGFGPAPAITKVLALAKLRLDQIDVIELNEAFAAQALAVTRAHGLADdDARVNPNGGAIALGHPLGASGARL 366
                                           *********************************************86679*********************** PP

                             TIGR01930 353 vltllkeLkergkkyGlatlCvggGqGaAvile 385
                                           v+  l+eL++ g++yGl t+C+g GqG+A+++e
  NCBI__GCF_000482785.1:WP_028311754.1 367 VIAALHELERTGGRYGLCTMCIGVGQGIALVIE 399
                                           *******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (401 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: 29.92
//
[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:

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