Alignments for a candidate for fadA in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Azospirillum brasilense Sp245

Align acetyl-CoA acetyltransferase (EC 2.3.1.16) (characterized)
to candidate AZOBR_RS30610 AZOBR_RS30610 acetyl-CoA acetyltransferase

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



>FitnessBrowser__azobra:AZOBR_RS30610
          Length = 391

 Score =  544 bits (1402), Expect = e-159
 Identities = 269/390 (68%), Positives = 321/390 (82%)

Query: 1   MTNVVIVSAARTAVGSFNGAFASTPAHDLGAAVIEAVVARAGIDKADVSETILGQVLTAG 60
           MT VVI SAART +GSFNGA +S PAH LG   I   ++RA  D A+V+E ILGQ+LTAG
Sbjct: 1   MTEVVIASAARTPIGSFNGALSSVPAHYLGEIAIREALSRAKTDAAEVTEVILGQILTAG 60

Query: 61  QGQNPARQAHIKAGLPQESAAWSINQVCGSGLRAVALAAQHVQLGDASIVVAGGQENMSL 120
           QGQNPARQA + AG+P  + A+ INQ+CGSGLR+VAL  Q ++ GDA ++V GGQE+MS 
Sbjct: 61  QGQNPARQAAVNAGIPASATAFGINQLCGSGLRSVALGYQAIRNGDAEVMVVGGQESMSQ 120

Query: 121 SPHVAHLRAGQKMGDLSFIDSMIKDGLWDAFNGYHMGQTAENVAAKWQISRDMQDEFAVA 180
           +PHV HLR G KMG    +D+M+KDGL DAF GYHMG TAENVA KWQ++R+ QD FA A
Sbjct: 121 APHVMHLRNGVKMGAAEMLDTMLKDGLMDAFKGYHMGTTAENVAQKWQLTREEQDVFAAA 180

Query: 181 SQNKAEAAQKAGRFADEIVPFVIKTRKGDVTVDADEYIRHGATLDAMAKLRPAFIKDGTV 240
           SQ KAEAAQK+GRF DEI+P  IK RKGD+ V  DEY +HG T +++AKLRPAF K+GTV
Sbjct: 181 SQQKAEAAQKSGRFKDEIIPVTIKGRKGDIIVADDEYPKHGTTAESLAKLRPAFSKEGTV 240

Query: 241 TAANASGINDGAAAVLVMSAEEAEKRGLSPLARIASYATAGLDPSIMGVGPIHASRKALE 300
           TA NASGINDGAAA+++M+AE A +RGL+PLARI S+ATAG+DP+IMG GPI ASR ALE
Sbjct: 241 TAGNASGINDGAAALVLMTAENAARRGLTPLARIVSWATAGVDPAIMGTGPIPASRLALE 300

Query: 301 KAGWKVGDLDLVEANEAFAAQACAVNKDMGWDPSIVNVNGGAIAIGHPIGASGARVLNTL 360
           KAGWK  DLDL+EANEAFAAQA AVNKD+GWD S VNVNGGAIA+GHP+GASGARVL TL
Sbjct: 301 KAGWKHDDLDLIEANEAFAAQALAVNKDLGWDTSKVNVNGGAIALGHPVGASGARVLTTL 360

Query: 361 LFEMQRRNAKKGLATLCIGGGMGVAMCLER 390
           L+EMQ+R+AKKGLATLCIGGGMG+A+ +ER
Sbjct: 361 LYEMQKRDAKKGLATLCIGGGMGIALTVER 390


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: 461
Number of extensions: 11
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 AZOBR_RS30610 AZOBR_RS30610 (acetyl-CoA 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.931181.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.4e-148  479.2  10.3   5.1e-148  479.0  10.3    1.0  1  FitnessBrowser__azobra:AZOBR_RS30610  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__azobra:AZOBR_RS30610  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  479.0  10.3  5.1e-148  5.1e-148       1     385 []       6     389 ..       6     389 .. 0.98

  Alignments for each domain:
  == domain 1  score: 479.0 bits;  conditional E-value: 5.1e-148
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 
                                           i +a+Rtpig+++g+l++++a+ L++ +i+e+l ra+ d++++ evilG+ l+ag+++n+aR+aa++ag+p s
  FitnessBrowser__azobra:AZOBR_RS30610   6 IASAARTPIGSFNGALSSVPAHYLGEIAIREALSRAKTDAAEVTEVILGQILTAGQGQNPARQAAVNAGIPAS 78 
                                           789********************************************************************** PP

                             TIGR01930  74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144
                                             a+ +n++C+Sgl++val++q+i+ G+a+v+v+GG EsmS++p++++    r+++k+g+a++ d++lkd+  
  FitnessBrowser__azobra:AZOBR_RS30610  79 ATAFGINQLCGSGLRSVALGYQAIRNGDAEVMVVGGQESMSQAPHVMHL---RNGVKMGAAEMLDTMLKDGlm 148
                                           ********************************************98886...59******************* PP

                             TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpn 214
                                            + ++++mg+tAen+a+k++++ReeqD +a++S+qka++A+++g+fkdei+pv++kg+  + +v++De ++ +
  FitnessBrowser__azobra:AZOBR_RS30610 149 dAFKGYHMGTTAENVAQKWQLTREEQDVFAAASQQKAEAAQKSGRFKDEIIPVTIKGRkgDIIVADDEYPKHG 221
                                           *999******************************************************999999********* PP

                             TIGR01930 215 ttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpv 287
                                           tt+e+LakL+paf + +g tvtAgN+s++nDGAaal+lm+ e a++ gltplarivs+a+agvdp++mg+gp+
  FitnessBrowser__azobra:AZOBR_RS30610 222 TTAESLAKLRPAFSK-EG-TVTAGNASGINDGAAALVLMTAENAARRGLTPLARIVSWATAGVDPAIMGTGPI 292
                                           *************95.8*.6***************************************************** PP

                             TIGR01930 288 pAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeL 360
                                           pA++ aL+kag++ +d+dl+E nEAFAaq+lav+k+lg  d++kvNvnGGAiAlGHP+GasGar+++tll+e+
  FitnessBrowser__azobra:AZOBR_RS30610 293 PASRLALEKAGWKHDDLDLIEANEAFAAQALAVNKDLG-WDTSKVNVNGGAIALGHPVGASGARVLTTLLYEM 364
                                           **************************************.88******************************** PP

                             TIGR01930 361 kergkkyGlatlCvggGqGaAvile 385
                                           ++r++k GlatlC+ggG+G+A+ +e
  FitnessBrowser__azobra:AZOBR_RS30610 365 QKRDAKKGLATLCIGGGMGIALTVE 389
                                           *********************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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 24.44
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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