Alignments for a candidate for fadA in Rhodospirillum rubrum ATCC 11170

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Rhodospirillum rubrum ATCC 11170

Align acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized)
to candidate YP_426468.1 Rru_A1380 acetyl-CoA acetyltransferase

Query= reanno::Phaeo:GFF329
         (391 letters)



>NCBI__GCF_000013085.1:YP_426468.1
          Length = 391

 Score =  546 bits (1406), Expect = e-160
 Identities = 271/390 (69%), Positives = 320/390 (82%)

Query: 1   MTNVVIASAARTAVGSFGGAFAKTPAHDLGAAVLQAVVERAGIDKSEVSETILGQVLTAA 60
           M +VVIA AARTA+G+F GAF   PAH LG   ++  + RA ++  +V E +LG VLTA 
Sbjct: 1   MNDVVIAGAARTAIGAFNGAFGAVPAHTLGEVAIREALNRAKVEAGDVDEVVLGHVLTAG 60

Query: 61  QGQNPARQAHINAGLPQESAAWSLNQVCGSGLRAVALAAQHIQLGDAAIVCAGGQENMTL 120
           QGQNPARQA +NAG+P E  A+ +NQ+CGSGLR VAL  Q I+ GDA IV AGGQE+M++
Sbjct: 61  QGQNPARQAAVNAGIPVERTAYCINQLCGSGLRTVALGFQAIRNGDAKIVVAGGQESMSM 120

Query: 121 SPHAANLRAGHKMGDMSYIDTMIRDGLWDAFNGYHMGQTAENVAEKWQISREMQDEFAVA 180
           +PHA++LRAG KMG    +DTMI+DGLWDAFNGYHMG TAEN+A+KWQISR  QDEFA A
Sbjct: 121 APHASHLRAGIKMGPGELVDTMIKDGLWDAFNGYHMGTTAENIADKWQISRAEQDEFACA 180

Query: 181 SQNKAEAAQKAGKFADEIAAFTVKTRKGDIIVDQDEYIRHGATIEAMQKLRPAFAKDGSV 240
           SQNKAEAA  AGKF DEIAA T+KTRKGD++VD DE+ + G TIE++ K R AF KDG+V
Sbjct: 181 SQNKAEAAIAAGKFKDEIAAVTLKTRKGDVVVDTDEHPKAGVTIESLAKARAAFRKDGTV 240

Query: 241 TAANASGLNDGAAATLLMSADDAEKRGIEPLARIASYATAGLDPSIMGVGPIYASRKALE 300
           TA NASG+NDGAAA +LMSAD+A  RGI PLARI S+ATAG+DP+IMG GPI ASR AL+
Sbjct: 241 TAGNASGINDGAAALVLMSADNARLRGIAPLARIVSWATAGVDPAIMGSGPIPASRLALK 300

Query: 301 KAGWSVDDLDLVEANEAFAAQACAVNKDMGWDPAIVNVNGGAIAIGHPIGASGCRVLNTL 360
           KAGW++DDLDL+EANEAFAAQA AVN+DMGWD A VNVNGGAIA+GHPIGASG RVL TL
Sbjct: 301 KAGWTIDDLDLIEANEAFAAQAIAVNRDMGWDTAKVNVNGGAIALGHPIGASGARVLVTL 360

Query: 361 LFEMKRRDAKKGLATLCIGGGMGVAMCVER 390
           L EM +RDAKKGL TLCIGGGMG+A+CVER
Sbjct: 361 LHEMIKRDAKKGLTTLCIGGGMGIALCVER 390


Lambda     K      H
   0.316    0.130    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: 490
Number of extensions: 12
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 YP_426468.1 Rru_A1380 (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.7693.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-141  458.0  12.0   1.4e-141  457.8  12.0    1.0  1  lcl|NCBI__GCF_000013085.1:YP_426468.1  Rru_A1380 acetyl-CoA acetyltrans


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000013085.1:YP_426468.1  Rru_A1380 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  457.8  12.0  1.4e-141  1.4e-141       1     385 []       6     389 ..       6     389 .. 0.98

  Alignments for each domain:
  == domain 1  score: 457.8 bits;  conditional E-value: 1.4e-141
                              TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpe 72 
                                            i +a+Rt+ig+++g++  ++a++L++ +i+e+l+ra++++ ++dev+lG+vl+ag+++n+aR+aa++ag+p 
  lcl|NCBI__GCF_000013085.1:YP_426468.1   6 IAGAARTAIGAFNGAFGAVPAHTLGEVAIREALNRAKVEAGDVDEVVLGHVLTAGQGQNPARQAAVNAGIPV 77 
                                            7899******************************************************************** PP

                              TIGR01930  73 svpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl 144
                                            +  a+ +n++C+Sgl++val+ q+i+ G+a++vvaGG EsmS +p+ ++    r+++k+g  +l d+++kd+
  lcl|NCBI__GCF_000013085.1:YP_426468.1  78 ERTAYCINQLCGSGLRTVALGFQAIRNGDAKIVVAGGQESMSMAPHASHL---RAGIKMGPGELVDTMIKDG 146
                                            *********************************************86665...69***************** PP

                              TIGR01930 145 ...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegi 211
                                               + ++++mg+tAen+a+k++isR eqDe+a +S++ka++Ai++gkfkdei  v++k++  ++vv++De++
  lcl|NCBI__GCF_000013085.1:YP_426468.1 147 lwdAFNGYHMGTTAENIADKWQISRAEQDEFACASQNKAEAAIAAGKFKDEIAAVTLKTRkgDVVVDTDEHP 218
                                            ***99*****************************************************99999********* PP

                              TIGR01930 212 rpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemg 283
                                            ++++t+e+Lak ++af++ +g tvtAgN+s++nDGAaal+lms + a+  g+ plarivs+a+agvdp++mg
  lcl|NCBI__GCF_000013085.1:YP_426468.1 219 KAGVTIESLAKARAAFRK-DG-TVTAGNASGINDGAAALVLMSADNARLRGIAPLARIVSWATAGVDPAIMG 288
                                            ****************95.9*.6************************************************* PP

                              TIGR01930 284 lgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivlt 355
                                             gp+pA++ aLkkag++i+d+dl+E nEAFAaq++av++++g  d++kvNvnGGAiAlGHP+GasGar+++t
  lcl|NCBI__GCF_000013085.1:YP_426468.1 289 SGPIPASRLALKKAGWTIDDLDLIEANEAFAAQAIAVNRDMG-WDTAKVNVNGGAIALGHPIGASGARVLVT 359
                                            ******************************************.88*************************** PP

                              TIGR01930 356 llkeLkergkkyGlatlCvggGqGaAvile 385
                                            ll+e+ +r++k Gl+tlC+ggG+G+A+ +e
  lcl|NCBI__GCF_000013085.1:YP_426468.1 360 LLHEMIKRDAKKGLTTLCIGGGMGIALCVE 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: 00:00:00.01
# Mc/sec: 8.41
//
[ok]

This GapMind analysis is from Sep 24 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