GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Methylocystis bryophila S285

Align acetyl-CoA acetyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_085770214.1 B1812_RS02620 acetyl-CoA C-acetyltransferase

Query= metacyc::MONOMER-13585
         (391 letters)



>NCBI__GCF_002117405.1:WP_085770214.1
          Length = 391

 Score =  587 bits (1514), Expect = e-172
 Identities = 293/389 (75%), Positives = 339/389 (87%)

Query: 2   TNVVIVSAARTAVGSFNGAFASTPAHDLGAAVIEAVVARAGIDKADVSETILGQVLTAGQ 61
           T++VIVSAARTAVGSFNGAF   PAH+LGAA +++ + RA +  ++V E ILGQVL A Q
Sbjct: 3   TDIVIVSAARTAVGSFNGAFGGVPAHELGAAAVKSALERAKVAPSEVCEVILGQVLGAAQ 62

Query: 62  GQNPARQAHIKAGLPQESAAWSINQVCGSGLRAVALAAQHVQLGDASIVVAGGQENMSLS 121
           GQNPARQA IKAG+P  + A+ INQVCGSGLRAVALAAQ +Q GDA IVVAGGQE+MSLS
Sbjct: 63  GQNPARQAAIKAGVPDSATAFGINQVCGSGLRAVALAAQQIQAGDAQIVVAGGQESMSLS 122

Query: 122 PHVAHLRAGQKMGDLSFIDSMIKDGLWDAFNGYHMGQTAENVAAKWQISRDMQDEFAVAS 181
            H AH+RAG KMG +SF D+MI DGL DAFN YHMG TAENVAAKWQISR  QD FAVAS
Sbjct: 123 THAAHMRAGTKMGPVSFADTMIIDGLTDAFNNYHMGITAENVAAKWQISRAEQDAFAVAS 182

Query: 182 QNKAEAAQKAGRFADEIVPFVIKTRKGDVTVDADEYIRHGATLDAMAKLRPAFIKDGTVT 241
           QNKAEAAQKAG+F DEI+P+ I TRKGDV VD+DEY++HG TL++++KLRPAF KDGTVT
Sbjct: 183 QNKAEAAQKAGKFKDEILPYTISTRKGDVVVDSDEYVKHGVTLESVSKLRPAFTKDGTVT 242

Query: 242 AANASGINDGAAAVLVMSAEEAEKRGLSPLARIASYATAGLDPSIMGVGPIHASRKALEK 301
           AANASG+NDGAAA++VMSA EA+KRGL PLARIA++ATAG+DPSIMG GPI A+RKALEK
Sbjct: 243 AANASGLNDGAAALVVMSAAEAKKRGLEPLARIAAWATAGVDPSIMGSGPIPATRKALEK 302

Query: 302 AGWKVGDLDLVEANEAFAAQACAVNKDMGWDPSIVNVNGGAIAIGHPIGASGARVLNTLL 361
           AGWKV DL+LVEANEAFAAQA AVNKD+GWDP+IVNVNGGAIAIGHPIGASGAR+L TLL
Sbjct: 303 AGWKVSDLNLVEANEAFAAQAIAVNKDLGWDPAIVNVNGGAIAIGHPIGASGARILTTLL 362

Query: 362 FEMQRRNAKKGLATLCIGGGMGVAMCLER 390
           +E++RR   KGLATLCIGGGMG+A+ +ER
Sbjct: 363 YELKRRGGGKGLATLCIGGGMGIALAVER 391


Lambda     K      H
   0.317    0.130    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: 531
Number of extensions: 16
Number of successful extensions: 1
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: 391
Length of database: 391
Length adjustment: 31
Effective length of query: 360
Effective length of database: 360
Effective search space:   129600
Effective search space used:   129600
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_085770214.1 B1812_RS02620 (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.980008.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.8e-144  465.9  15.2   5.4e-144  465.8  15.2    1.0  1  NCBI__GCF_002117405.1:WP_085770214.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002117405.1:WP_085770214.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  465.8  15.2  5.4e-144  5.4e-144       1     385 []       7     390 ..       7     390 .. 0.98

  Alignments for each domain:
  == domain 1  score: 465.8 bits;  conditional E-value: 5.4e-144
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 
                                           iv+a+Rt++g+++g++  ++a++L+aa++k++lera++ p+++ evilG+vl a++++n+aR+aa++ag+p+s
  NCBI__GCF_002117405.1:WP_085770214.1   7 IVSAARTAVGSFNGAFGGVPAHELGAAAVKSALERAKVAPSEVCEVILGQVLGAAQGQNPARQAAIKAGVPDS 79 
                                           8************************************************************************ PP

                             TIGR01930  74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144
                                             a+ +n+vC+Sgl+Avalaaq+i+aG+a++vvaGG EsmS + +  ++   r++ k+g  + +d+++ d+  
  NCBI__GCF_002117405.1:WP_085770214.1  80 ATAFGINQVCGSGLRAVALAAQQIQAGDAQIVVAGGQESMSLSTHAAHM---RAGTKMGPVSFADTMIIDGlt 149
                                           ******************************************9987777...588999999999999999999 PP

                             TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpn 214
                                            + ++++mg+tAen+a+k++isR eqD++a++S++ka++A+++gkfkdei+p+++ ++  ++vv++De ++ +
  NCBI__GCF_002117405.1:WP_085770214.1 150 dAFNNYHMGITAENVAAKWQISRAEQDAFAVASQNKAEAAQKAGKFKDEILPYTISTRkgDVVVDSDEYVKHG 222
                                           999****************************************************999999************ PP

                             TIGR01930 215 ttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpv 287
                                           +tle+++kL+paf++ +g tvtA+N+s+lnDGAaal++ms + ak+ gl+plari ++a+agvdp++mg gp+
  NCBI__GCF_002117405.1:WP_085770214.1 223 VTLESVSKLRPAFTK-DG-TVTAANASGLNDGAAALVVMSAAEAKKRGLEPLARIAAWATAGVDPSIMGSGPI 293
                                           *************95.9*.6***************************************************** PP

                             TIGR01930 288 pAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeL 360
                                           pA++kaL+kag+++sd++lvE nEAFAaq++av+k+lg  d++ vNvnGGAiA+GHP+GasGari++tll+eL
  NCBI__GCF_002117405.1:WP_085770214.1 294 PATRKALEKAGWKVSDLNLVEANEAFAAQAIAVNKDLG-WDPAIVNVNGGAIAIGHPIGASGARILTTLLYEL 365
                                           **************************************.88******************************** PP

                             TIGR01930 361 kergkkyGlatlCvggGqGaAvile 385
                                           k+rg+  GlatlC+ggG+G+A+ +e
  NCBI__GCF_002117405.1:WP_085770214.1 366 KRRGGGKGLATLCIGGGMGIALAVE 390
                                           *********************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (391 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 25.58
//
[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