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

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.19217.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.57
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources