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_426557.1 Rru_A1469 acetyl-CoA acetyltransferase

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



>NCBI__GCF_000013085.1:YP_426557.1
          Length = 391

 Score =  525 bits (1353), Expect = e-154
 Identities = 260/391 (66%), Positives = 317/391 (81%)

Query: 1   MTNVVIASAARTAVGSFGGAFAKTPAHDLGAAVLQAVVERAGIDKSEVSETILGQVLTAA 60
           M ++VIA+AARTAVG+F G+ +  PAH LGA+V+  ++ R  I   E+ + +LGQVLTAA
Sbjct: 1   MNDIVIAAAARTAVGAFTGSLSSLPAHSLGASVITDLLTRGKIAAGEIDDVLLGQVLTAA 60

Query: 61  QGQNPARQAHINAGLPQESAAWSLNQVCGSGLRAVALAAQHIQLGDAAIVCAGGQENMTL 120
           QGQNPARQA I AGLP  S A ++NQVCGSGLRAVAL AQ I  GDA +V AGGQE+M+L
Sbjct: 61  QGQNPARQAAIAAGLPASSTALTINQVCGSGLRAVALGAQAIACGDAEVVIAGGQESMSL 120

Query: 121 SPHAANLRAGHKMGDMSYIDTMIRDGLWDAFNGYHMGQTAENVAEKWQISREMQDEFAVA 180
           +PHA  LRAG KMG    +DTMI+DGLW+AF+GYHMG TAE VA+ + I R  QD FA+A
Sbjct: 121 APHAVLLRAGVKMGPAEMVDTMIKDGLWEAFHGYHMGITAETVAQAFGIDRATQDAFALA 180

Query: 181 SQNKAEAAQKAGKFADEIAAFTVKTRKGDIIVDQDEYIRHGATIEAMQKLRPAFAKDGSV 240
           SQ KA AAQ+ G+F DEI A  V++RKG+++VD DE+++   T +++ KLRPAF KDG+V
Sbjct: 181 SQQKAAAAQREGRFVDEIVAVCVRSRKGEVLVDSDEHLKPDTTAQSLAKLRPAFTKDGTV 240

Query: 241 TAANASGLNDGAAATLLMSADDAEKRGIEPLARIASYATAGLDPSIMGVGPIYASRKALE 300
           TA NASGLNDGAA  LLMSA++A KRG+ PLAR+ S+ATAG+DP++MG GPI ASRKAL 
Sbjct: 241 TAGNASGLNDGAAGVLLMSAENAAKRGVTPLARVVSWATAGVDPAVMGTGPIPASRKALA 300

Query: 301 KAGWSVDDLDLVEANEAFAAQACAVNKDMGWDPAIVNVNGGAIAIGHPIGASGCRVLNTL 360
           KAGW++DDLDL+EANEAFAAQA AVN++MGWD A VNVNGGAIAIGHPIGASG R+L +L
Sbjct: 301 KAGWTIDDLDLIEANEAFAAQAIAVNREMGWDTAKVNVNGGAIAIGHPIGASGARILVSL 360

Query: 361 LFEMKRRDAKKGLATLCIGGGMGVAMCVERP 391
           L EM RRDAKK LATLCIGGGMG+A+CVERP
Sbjct: 361 LHEMTRRDAKKALATLCIGGGMGIALCVERP 391


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: 471
Number of extensions: 9
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_426557.1 Rru_A1469 (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.1646.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   1.9e-143  463.9  15.1   2.3e-143  463.7  15.1    1.0  1  lcl|NCBI__GCF_000013085.1:YP_426557.1  Rru_A1469 acetyl-CoA acetyltrans


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000013085.1:YP_426557.1  Rru_A1469 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  463.7  15.1  2.3e-143  2.3e-143       1     385 []       6     389 ..       6     389 .. 0.98

  Alignments for each domain:
  == domain 1  score: 463.7 bits;  conditional E-value: 2.3e-143
                              TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpe 72 
                                            i +a+Rt++g+++gsl++l+a++L+a vi  ll r ++ + +id+v lG+vl+a++++n+aR+aa+aaglp 
  lcl|NCBI__GCF_000013085.1:YP_426557.1   6 IAAAARTAVGAFTGSLSSLPAHSLGASVITDLLTRGKIAAGEIDDVLLGQVLTAAQGQNPARQAAIAAGLPA 77 
                                            789********************************************************************* PP

                              TIGR01930  73 svpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl 144
                                            s  alt+n+vC+Sgl+Aval+aq+i++G+a+vv+aGG EsmS +p+ +     r+++k+g a++ d+++kd+
  lcl|NCBI__GCF_000013085.1:YP_426557.1  78 SSTALTINQVCGSGLRAVALGAQAIACGDAEVVIAGGQESMSLAPHAVLL---RAGVKMGPAEMVDTMIKDG 146
                                            *********************************************98876...69***************** PP

                              TIGR01930 145 ...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegi 211
                                               + ++++mg+tAe++a+ +gi R +qD++al+S+qkaa+A++eg+f deiv v v+ +  ++ v++De++
  lcl|NCBI__GCF_000013085.1:YP_426557.1 147 lweAFHGYHMGITAETVAQAFGIDRATQDAFALASQQKAAAAQREGRFVDEIVAVCVRSRkgEVLVDSDEHL 218
                                            ***99***************************************************99999999******** PP

                              TIGR01930 212 rpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemg 283
                                            +p+tt+++LakL+paf++ +g tvtAgN+s+lnDGAa +llms e a++ g+tplar+vs+a+agvdp++mg
  lcl|NCBI__GCF_000013085.1:YP_426557.1 219 KPDTTAQSLAKLRPAFTK-DG-TVTAGNASGLNDGAAGVLLMSAENAAKRGVTPLARVVSWATAGVDPAVMG 288
                                            ****************95.9*.6************************************************* PP

                              TIGR01930 284 lgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivlt 355
                                            +gp+pA++kaL+kag++i+d+dl+E nEAFAaq++av++e+g  d++kvNvnGGAiA+GHP+GasGari+++
  lcl|NCBI__GCF_000013085.1:YP_426557.1 289 TGPIPASRKALAKAGWTIDDLDLIEANEAFAAQAIAVNREMG-WDTAKVNVNGGAIAIGHPIGASGARILVS 359
                                            ******************************************.88*************************** PP

                              TIGR01930 356 llkeLkergkkyGlatlCvggGqGaAvile 385
                                            ll+e+ +r++k +latlC+ggG+G+A+ +e
  lcl|NCBI__GCF_000013085.1:YP_426557.1 360 LLHEMTRRDAKKALATLCIGGGMGIALCVE 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: 11.01
//
[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