Alignments for a candidate for fadA in Rhizobium leguminosarum WSM1325

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Rhizobium leguminosarum WSM1325

Align acetyl-CoA acetyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_012759437.1 RLEG_RS20540 acetyl-CoA C-acetyltransferase

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



>NCBI__GCF_000023185.1:WP_012759437.1
          Length = 393

 Score =  610 bits (1573), Expect = e-179
 Identities = 299/387 (77%), Positives = 339/387 (87%)

Query: 3   NVVIVSAARTAVGSFNGAFASTPAHDLGAAVIEAVVARAGIDKADVSETILGQVLTAGQG 62
           ++VI SA RTAVG+FNGAFA+  AH+LGAAVI+  + RAG+D  +V E ILGQVL AG+G
Sbjct: 5   SIVIASAGRTAVGAFNGAFATVLAHELGAAVIKGALERAGVDAGEVDEVILGQVLAAGEG 64

Query: 63  QNPARQAHIKAGLPQESAAWSINQVCGSGLRAVALAAQHVQLGDASIVVAGGQENMSLSP 122
           QNPARQA +KAG+PQE+ AW +NQ+CGSGLRAVAL  Q +  GDA I+VAGGQE+MS++P
Sbjct: 65  QNPARQAAMKAGIPQEATAWGVNQLCGSGLRAVALGMQQIATGDAKIIVAGGQESMSMAP 124

Query: 123 HVAHLRAGQKMGDLSFIDSMIKDGLWDAFNGYHMGQTAENVAAKWQISRDMQDEFAVASQ 182
           H AHLR G KMGD+  ID+MIKDGL DAF+GYHMG TAENVA +WQ+SRD QD+FAV+SQ
Sbjct: 125 HAAHLRGGVKMGDMKMIDTMIKDGLTDAFHGYHMGITAENVARQWQLSRDDQDQFAVSSQ 184

Query: 183 NKAEAAQKAGRFADEIVPFVIKTRKGDVTVDADEYIRHGATLDAMAKLRPAFIKDGTVTA 242
           NKAEAAQKAGRF DEI+P+VIKTRKGDVTVDADEYIRHGAT++AM KLRPAF KDGTVTA
Sbjct: 185 NKAEAAQKAGRFVDEIIPYVIKTRKGDVTVDADEYIRHGATIEAMGKLRPAFDKDGTVTA 244

Query: 243 ANASGINDGAAAVLVMSAEEAEKRGLSPLARIASYATAGLDPSIMGVGPIHASRKALEKA 302
           ANASG+NDGAA  ++MS  EA +RG+ PLARI S+ATAG+DP IMG GPI ASRKALEKA
Sbjct: 245 ANASGLNDGAAVAVLMSEAEAVRRGVQPLARIVSWATAGVDPQIMGTGPIPASRKALEKA 304

Query: 303 GWKVGDLDLVEANEAFAAQACAVNKDMGWDPSIVNVNGGAIAIGHPIGASGARVLNTLLF 362
           GW V DLDLVEANEAFAAQACAV KD+GWDPSIVNVNGGAIAIGHPIGASGARVLNTLLF
Sbjct: 305 GWSVNDLDLVEANEAFAAQACAVTKDLGWDPSIVNVNGGAIAIGHPIGASGARVLNTLLF 364

Query: 363 EMQRRNAKKGLATLCIGGGMGVAMCLE 389
           EM+RR AKKGLATLCIGGGMGVAMC E
Sbjct: 365 EMKRRGAKKGLATLCIGGGMGVAMCFE 391


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: 578
Number of extensions: 14
Number of successful extensions: 2
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: 393
Length adjustment: 31
Effective length of query: 360
Effective length of database: 362
Effective search space:   130320
Effective search space used:   130320
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_012759437.1 RLEG_RS20540 (acetyl-CoA C-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.10220.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.7e-145  469.3  12.3   5.5e-145  469.0  12.3    1.0  1  lcl|NCBI__GCF_000023185.1:WP_012759437.1  RLEG_RS20540 acetyl-CoA C-acetyl


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000023185.1:WP_012759437.1  RLEG_RS20540 acetyl-CoA C-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  469.0  12.3  5.5e-145  5.5e-145       1     385 []       8     391 ..       8     391 .. 0.98

  Alignments for each domain:
  == domain 1  score: 469.0 bits;  conditional E-value: 5.5e-145
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 
                                               i +a Rt++g+++g+++++ a++L+aavik++lerag+d+ ++devilG+vl age++n+aR+aa++ag
  lcl|NCBI__GCF_000023185.1:WP_012759437.1   8 IASAGRTAVGAFNGAFATVLAHELGAAVIKGALERAGVDAGEVDEVILGQVLAAGEGQNPARQAAMKAG 76 
                                               78899**************************************************************** PP

                                 TIGR01930  70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138
                                               +p++  a+ vn++C+Sgl+Aval++q+i++G+a+++vaGG EsmS +p+  +    r ++k+g++k+ d
  lcl|NCBI__GCF_000023185.1:WP_012759437.1  77 IPQEATAWGVNQLCGSGLRAVALGMQQIATGDAKIIVAGGQESMSMAPHAAHL---RGGVKMGDMKMID 142
                                               ************************************************86665...69*********** PP

                                 TIGR01930 139 qllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..k 202
                                               +++kd+   + ++++mg+tAen+a+++++sR++qD++a++S++ka++A+++g+f dei+p+++k++  +
  lcl|NCBI__GCF_000023185.1:WP_012759437.1 143 TMIKDGltdAFHGYHMGITAENVARQWQLSRDDQDQFAVSSQNKAEAAQKAGRFVDEIIPYVIKTRkgD 211
                                               *******99999***************************************************999999 PP

                                 TIGR01930 203 kvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivs 271
                                               ++v+ De ir + t+e+++kL+paf++ +g tvtA+N+s+lnDGAa+++lmse+ a + g++plarivs
  lcl|NCBI__GCF_000023185.1:WP_012759437.1 212 VTVDADEYIRHGATIEAMGKLRPAFDK-DG-TVTAANASGLNDGAAVAVLMSEAEAVRRGVQPLARIVS 278
                                               *************************95.9*.6************************************* PP

                                 TIGR01930 272 aavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiA 340
                                               +a+agvdp++mg+gp+pA++kaL+kag+s++d+dlvE nEAFAaq+ av+k+lg  d++ vNvnGGAiA
  lcl|NCBI__GCF_000023185.1:WP_012759437.1 279 WATAGVDPQIMGTGPIPASRKALEKAGWSVNDLDLVEANEAFAAQACAVTKDLG-WDPSIVNVNGGAIA 346
                                               ******************************************************.88************ PP

                                 TIGR01930 341 lGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               +GHP+GasGar++ tll e+k+rg+k GlatlC+ggG+G+A+ +e
  lcl|NCBI__GCF_000023185.1:WP_012759437.1 347 IGHPIGASGARVLNTLLFEMKRRGAKKGLATLCIGGGMGVAMCFE 391
                                               ******************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (393 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: 8.46
//
[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