GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Magnetospirillum magneticum AMB-1

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_011384976.1 AMB_RS13060 acetyl-CoA C-acyltransferase

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



>NCBI__GCF_000009985.1:WP_011384976.1
          Length = 398

 Score =  426 bits (1095), Expect = e-124
 Identities = 223/400 (55%), Positives = 289/400 (72%), Gaps = 2/400 (0%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           M D +I D +R+PIGR GG LA VR+DDLAA  ++AL+  + + + + V++V  GC NQA
Sbjct: 1   MLDAYIYDGLRSPIGRHGGGLAPVRSDDLAAEVIRALVARS-SFKPEDVEDVILGCTNQA 59

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           GED+RNVAR A LLAGLP  + G T+NRLCASG+ A+  A R++  GE +L +AGGVESM
Sbjct: 60  GEDSRNVARHAALLAGLPVEVAGQTVNRLCASGLAAVLDAARSVTCGEGDLYLAGGVESM 119

Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180
           +RAPFV+ K +S +SR+ ++ DTTIG RF NP +   +G  SMPETADN+A D  +SR  
Sbjct: 120 TRAPFVLAKGDSAWSRDARIFDTTIGARFANPKVVKSFGGHSMPETADNIAHDLGLSREA 179

Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKPV 240
            DAFA  SQ K A A+A GF+  EI P+ IA +KG+TIV  DEH RP+T L ALTKLKP+
Sbjct: 180 SDAFAAASQAKYAKAKAEGFYEGEIHPITIAGRKGDTIVAEDEHPRPQTDLAALTKLKPL 239

Query: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVP 300
                 VTAGNASG+NDGAAAL + S  A +K G+ P AR++  A+ GV PRVMG+GPVP
Sbjct: 240 -FEGGVVTAGNASGINDGAAALFIGSRAAGEKAGIAPIARIVAGAAAGVPPRVMGLGPVP 298

Query: 301 AVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM 360
           A+ K   R  +++ D D+IE+NEAFA Q L  + +LGVA D  ++NPNGGAIA+GHPLG 
Sbjct: 299 AITKALARAKLSLKDLDLIEINEAFAVQVLGCVTQLGVAADDSRLNPNGGAIAIGHPLGC 358

Query: 361 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           SGARL LTA  QL+++GGR  + ++C+GVG GLA  IERV
Sbjct: 359 SGARLALTAARQLQRTGGRHAVVSLCIGVGHGLAAVIERV 398


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: 508
Number of extensions: 18
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: 400
Length of database: 398
Length adjustment: 31
Effective length of query: 369
Effective length of database: 367
Effective search space:   135423
Effective search space used:   135423
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_011384976.1 AMB_RS13060 (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.16888.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     2e-132  427.7   3.0   2.2e-132  427.5   3.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011384976.1  AMB_RS13060 acetyl-CoA C-acyltra


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011384976.1  AMB_RS13060 acetyl-CoA C-acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.5   3.0  2.2e-132  2.2e-132       1     385 []       6     396 ..       6     396 .. 0.96

  Alignments for each domain:
  == domain 1  score: 427.5 bits;  conditional E-value: 2.2e-132
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaa 68 
                                               i+d++R+pig+ gg l+ ++++dL+a+vi++l++r+ ++pe++++vilG++ qage+  n+aR+aal a
  lcl|NCBI__GCF_000009985.1:WP_011384976.1   6 IYDGLRSPIGRHGGGLAPVRSDDLAAEVIRALVARSSFKPEDVEDVILGCTNQAGEDsRNVARHAALLA 74 
                                               899*******99********************************************************* PP

                                 TIGR01930  69 glpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakle 137
                                               glp +v++ tvnr+CaSgl+Av +aa+++ +Ge d+++aGGvEsm+r+p++l +  +++s + + +++ 
  lcl|NCBI__GCF_000009985.1:WP_011384976.1  75 GLPVEVAGQTVNRLCASGLAAVLDAARSVTCGEGDLYLAGGVESMTRAPFVLAKGDSAWSRDARIFDTT 143
                                               *****************************************************9988888887776665 PP

                                 TIGR01930 138 dqllkdl.......vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevk 199
                                                 +   +       +  + sm etA+n+a++ g+sRe  D++a++S+ k akA +eg+ + ei p+++ 
  lcl|NCBI__GCF_000009985.1:WP_011384976.1 144 IGAR--FanpkvvkSFGGHSMPETADNIAHDLGLSREASDAFAAASQAKYAKAKAEGFYEGEIHPITIA 210
                                               5333..134778898899*************************************************** PP

                                 TIGR01930 200 gk..kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltpl 266
                                               g+  +++v++De++rp+t l++L kLkp f+   g +vtAgN+s++nDGAaal + s+++ ++ g+ p+
  lcl|NCBI__GCF_000009985.1:WP_011384976.1 211 GRkgDTIVAEDEHPRPQTDLAALTKLKPLFE--GG-VVTAGNASGINDGAAALFIGSRAAGEKAGIAPI 276
                                               *99999************************7..58.8******************************** PP

                                 TIGR01930 267 arivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsld.lekvNv 334
                                               ariv+ a agv+p++mglgpvpAi+kaL++a+ls++d+dl+EinEAFA+qvl ++++lg  + ++++N 
  lcl|NCBI__GCF_000009985.1:WP_011384976.1 277 ARIVAGAAAGVPPRVMGLGPVPAITKALARAKLSLKDLDLIEINEAFAVQVLGCVTQLGVAAdDSRLNP 345
                                               ***********************************************************8556****** PP

                                 TIGR01930 335 nGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               nGGAiA+GHPlG+sGar+ lt +++L++ g++ ++++lC+g G G A+++e
  lcl|NCBI__GCF_000009985.1:WP_011384976.1 346 NGGAIAIGHPLGCSGARLALTAARQLQRTGGRHAVVSLCIGVGHGLAAVIE 396
                                               *************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (398 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: 9.45
//
[ok]

This GapMind analysis is from Sep 17 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