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 3-ketoacyl-CoA thiolase (EC 2.3.1.16) (characterized)
to candidate AZOBR_RS28180 AZOBR_RS28180 acetyl-CoA acetyltransferase

Query= reanno::acidovorax_3H11:Ac3H11_2994
         (397 letters)



>FitnessBrowser__azobra:AZOBR_RS28180
          Length = 397

 Score =  501 bits (1291), Expect = e-146
 Identities = 248/389 (63%), Positives = 305/389 (78%)

Query: 7   DPIVIVGAARTPMGSLQGDFSSLAAHDLGGAAIKAAIERAGVSPDAVGEVLFGNCLMAGQ 66
           DP+VIV AARTP+G  QG+ S+L AH LG  A++AA+ RAG++P+ V EVL G  L AGQ
Sbjct: 6   DPVVIVSAARTPLGRFQGELSALPAHALGAHAVRAALSRAGLAPERVDEVLLGCVLPAGQ 65

Query: 67  GQAPARQAAFKGGLPKGAGAVTLSKMCGSGMKAAMMAHDMLLAGSHDVMVAGGMESMTNA 126
           GQAPARQAA   GLP   GA T++K+CGSGMKA M+AHD++ AGS D++VAGGMESM+NA
Sbjct: 66  GQAPARQAARGAGLPDATGATTVNKVCGSGMKATMLAHDLIRAGSADLVVAGGMESMSNA 125

Query: 127 PYLLQKGRGGYRLGHDRIFDHMMLDGLEDAYEAGRSMGTFGEDCAAKYSFTREQQDAFAT 186
           PYLL K RGGYR+GHDRI DH+MLDGLEDAYE GR MG FGE  A  Y FTR +QDA+A 
Sbjct: 126 PYLLAKARGGYRIGHDRILDHLMLDGLEDAYEGGRPMGDFGEATADLYGFTRAEQDAYAV 185

Query: 187 ASVQRAKAATESGAFAAEIVPVTVKTRAGETVVSVDEGPGKVKLEKIATLKPAFKKDGTI 246
            ++ RA+AA  SGAF AEI PVT+  + GE  V+ DE P KV  EKI  LKPAF++DGTI
Sbjct: 186 ETLTRARAAIASGAFTAEIAPVTLAVKGGERTVADDENPLKVAPEKIPALKPAFRRDGTI 245

Query: 247 TAASSSSINDGAAALVMMRESTAKKLGAKPLARIVSHATHAQEPEWFATAPLGATQKALA 306
           TAASSS+  DGAAAL++ R S A++ G   LA I+ HATH+Q+P WF TAP+ A +K L 
Sbjct: 246 TAASSSANADGAAALLLTRRSLAEREGLPVLATILGHATHSQDPAWFTTAPIPAIRKLLD 305

Query: 307 KAGWQVGDVQLWEINEAFAVVPMALMKELDLPHDKVNVNGGACALGHPIGASGARIMVTL 366
           + GW +GDV L+EINEAFAVV MA  ++L +P D +NVNGGACALGHPIGA+GAR++VTL
Sbjct: 306 RVGWGIGDVDLFEINEAFAVVAMAAQRDLGIPRDALNVNGGACALGHPIGATGARLIVTL 365

Query: 367 IHALKARGLTKGLATLCIGGGEATAVALE 395
           +HAL ARGL +G+A+LCIGGGEATA+A+E
Sbjct: 366 LHALAARGLRRGVASLCIGGGEATAIAVE 394


Lambda     K      H
   0.317    0.131    0.376 

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: 530
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: 397
Length of database: 397
Length adjustment: 31
Effective length of query: 366
Effective length of database: 366
Effective search space:   133956
Effective search space used:   133956
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_RS28180 AZOBR_RS28180 (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.17332.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-126  408.7   2.4   1.4e-126  408.5   2.4    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS28180  AZOBR_RS28180 acetyl-CoA acetylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS28180  AZOBR_RS28180 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  408.5   2.4  1.4e-126  1.4e-126       1     385 []      10     394 ..      10     394 .. 0.97

  Alignments for each domain:
  == domain 1  score: 408.5 bits;  conditional E-value: 1.4e-126
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 
                                               iv+a+Rtp g+++g l+ l+a+ L+a++++++l ragl pe++dev lG+vl+ag+++++aR+aa  ag
  lcl|FitnessBrowser__azobra:AZOBR_RS28180  10 IVSAARTPLGRFQGELSALPAHALGAHAVRAALSRAGLAPERVDEVLLGCVLPAGQGQAPARQAARGAG 78 
                                               8******************************************************************** PP

                                 TIGR01930  70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138
                                               lp+ + a+tvn+vC+Sg++A +la + i+aG ad+vvaGG+EsmS++p+ll ++  r ++++g+ +  d
  lcl|FitnessBrowser__azobra:AZOBR_RS28180  79 LPDATGATTVNKVCGSGMKATMLAHDLIRAGSADLVVAGGMESMSNAPYLLAKA--RGGYRIGHDRILD 145
                                               ***************************************************997..89*********** PP

                                 TIGR01930 139 qllkdl....vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk.. 201
                                               +l+ d+     + + +mg   e +a+ yg++R eqD+ya++  ++a +Ai++g f +ei pv++  k  
  lcl|FitnessBrowser__azobra:AZOBR_RS28180 146 HLMLDGledaYEGGRPMGDFGEATADLYGFTRAEQDAYAVETLTRARAAIASGAFTAEIAPVTLAVKgg 214
                                               99988899998999**************************************************99997 PP

                                 TIGR01930 202 kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplariv 270
                                               +++v++De++  ++  ek+  Lkpaf++ +g t+tA++ss  +DGAaalll+ ++ a++ gl +la+i 
  lcl|FitnessBrowser__azobra:AZOBR_RS28180 215 ERTVADDENPL-KVAPEKIPALKPAFRR-DG-TITAASSSANADGAAALLLTRRSLAEREGLPVLATIL 280
                                               77766666665.99************96.9*.6************************************ PP

                                 TIGR01930 271 saavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAi 339
                                               ++a+ + dp+ ++++p+pAi+k+L++ g+ i d+dl+EinEAFA++++a++++lg + ++ +NvnGGA 
  lcl|FitnessBrowser__azobra:AZOBR_RS28180 281 GHATHSQDPAWFTTAPIPAIRKLLDRVGWGIGDVDLFEINEAFAVVAMAAQRDLG-IPRDALNVNGGAC 348
                                               *******************************************************.88*********** PP

                                 TIGR01930 340 AlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               AlGHP+Ga+Gar+++tll++L+ rg ++G+a+lC+ggG ++A+ +e
  lcl|FitnessBrowser__azobra:AZOBR_RS28180 349 ALGHPIGATGARLIVTLLHALAARGLRRGVASLCIGGGEATAIAVE 394
                                               ******************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (397 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: 9.54
//
[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