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 3-ketoacyl-CoA thiolase; EC 2.3.1.16; Acetyl-CoA acyltransferase; Beta-ketothiolase; Fatty acid oxidation complex subunit beta (uncharacterized)
to candidate WP_012755967.1 RLEG_RS01225 acetyl-CoA acetyltransferase

Query= curated2:B7H1I1
         (390 letters)



>NCBI__GCF_000023185.1:WP_012755967.1
          Length = 402

 Score =  241 bits (616), Expect = 2e-68
 Identities = 154/405 (38%), Positives = 222/405 (54%), Gaps = 27/405 (6%)

Query: 8   DVVIVDGVRSAMGKSK-NGMFRNVRADSLSAELVRALVARNQFDVNEVEDLIWGCVNQTL 66
           +V I D VR+  G+ K +G    V +  L+A+ + A+  RN  D   V+D+I GCV+  +
Sbjct: 3   EVFIYDHVRTPRGRGKKDGALHEVPSVRLAAKTLEAIRDRNGLDTATVDDIIMGCVDPVM 62

Query: 67  EQGMNIGRNIGLLAGLPKTVAGQTVNRLCGSSMQAIHTAAAQIATNQGDIFIIGGVEHMG 126
           + G  I +     AG      G  ++R C S + A++  A +IA    DI I GGVE M 
Sbjct: 63  DAGAVIPKAAAFEAGYSTKAPGMQISRFCASGLDAVNFGAGKIAQGADDIVIAGGVESMS 122

Query: 127 HVGM-MHGIDLNPEASKHYAKASNMMGLTAEMLGRMNGITREEQDAFGVESHRRAWAATQ 185
            VG+ M G     + S ++       G++A+++    G +R + DA+ VES +RA  A +
Sbjct: 123 RVGLGMSGGAWFMDPSVNFPAYFMPQGVSADLIATKYGFSRTDVDAYAVESQKRAAHAWE 182

Query: 186 EGRFKNEIIGVEGHDANGFKILCDIDEVIRPDANLEAFKALKPVFDPKG--GSVTAA--- 240
           +G F   +I V+  D NG  IL   DE +RP  +++A  +L P F   G  G   A    
Sbjct: 183 KGWFDKSVIPVK--DQNGLTILAK-DEHMRPGTDMQALASLNPSFQMPGEMGGFEAVGIQ 239

Query: 241 ---------------TSSALSDGASAMLLMSAERAQALGLKPRAVIRSMAVAGCDAAIMG 285
                           SS + DGAS +LL S    Q++G KPRA I++ A  G D A+M 
Sbjct: 240 AHPEIERINYVHHAGNSSGIVDGASVVLLGSKAGGQSMGKKPRARIKAFANIGSDPALML 299

Query: 286 YGPVPATQKALKRAGLSIADIQTVELNEAFAAQGLSVLKGLGLYDKQDIVNLNGGAIALG 345
            GPV  T+K LKR+G+S++DI   ELNEAFAA  L  ++   +    D +N+NGGAIA+G
Sbjct: 300 TGPVDVTEKLLKRSGMSLSDIDLFELNEAFAAVVLRYMQAFDI--DHDRINVNGGAIAMG 357

Query: 346 HPLGCSGARITTTLLNVMEQQDTQIGLATMCIGLGQGIATVIERV 390
           HPLG +GA I  T+L+ +E++D    L T+CIG G G ATVIERV
Sbjct: 358 HPLGATGAMILGTVLDELERRDLNTALVTLCIGAGMGTATVIERV 402


Lambda     K      H
   0.318    0.134    0.381 

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: 374
Number of extensions: 21
Number of successful extensions: 5
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: 390
Length of database: 402
Length adjustment: 31
Effective length of query: 359
Effective length of database: 371
Effective search space:   133189
Effective search space used:   133189
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_012755967.1 RLEG_RS01225 (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.11533.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-124  401.6   0.3   1.9e-124  401.4   0.3    1.0  1  lcl|NCBI__GCF_000023185.1:WP_012755967.1  RLEG_RS01225 acetyl-CoA acetyltr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000023185.1:WP_012755967.1  RLEG_RS01225 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  401.4   0.3  1.9e-124  1.9e-124       1     385 []       6     400 ..       6     400 .. 0.95

  Alignments for each domain:
  == domain 1  score: 401.4 bits;  conditional E-value: 1.9e-124
                                 TIGR01930   1 ivdavRtpig..klggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaal 66 
                                               i+d vRtp g  k  g+l+e++++ L+a++++++ +r+gld + +d++i+G+v +  +  a i + aa+
  lcl|NCBI__GCF_000023185.1:WP_012755967.1   6 IYDHVRTPRGrgKKDGALHEVPSVRLAAKTLEAIRDRNGLDTATVDDIIMGCVDPVMDAgAVIPKAAAF 74 
                                               7899*******988********************************************99********* PP

                                 TIGR01930  67 aaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkak 135
                                               +ag +++ p+++++r+CaSgl+Av+ +a ki+ G+ d+v+aGGvEsmSrv ++++    ++ +++    
  lcl|NCBI__GCF_000023185.1:WP_012755967.1  75 EAGYSTKAPGMQISRFCASGLDAVNFGAGKIAQGADDIVIAGGVESMSRVGLGMSGG--AWFMDPS--V 139
                                               **************************************************9999987..7888882..2 PP

                                 TIGR01930 136 ledqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgkkkv 204
                                               +        +   +++g++A+ +a+kyg+sR+++D+ya++S+++aa+A+e+g f+++++pv+ ++  ++
  lcl|NCBI__GCF_000023185.1:WP_012755967.1 140 NF-------PAYFMPQGVSADLIATKYGFSRTDVDAYAVESQKRAAHAWEKGWFDKSVIPVKDQNGLTI 201
                                               22.......35689************************************************998899* PP

                                 TIGR01930 205 vskDegirpnttlekLakLkpafkekkgs....................tvtAgNssqlnDGAaalllm 253
                                               ++kDe++rp+t +++La+L+p f+   g+                    +++AgNss++ DGA+++ll 
  lcl|NCBI__GCF_000023185.1:WP_012755967.1 202 LAKDEHMRPGTDMQALASLNPSFQM-PGEmggfeavgiqahpeierinyVHHAGNSSGIVDGASVVLLG 269
                                               ***********************98.344455667777777888888889******************* PP

                                 TIGR01930 254 seevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavek 322
                                               s++  +++g +p ari ++a++g+dp+ m++gpv  +ek+Lk+ g+s+sdidl+E+nEAFAa+vl  ++
  lcl|NCBI__GCF_000023185.1:WP_012755967.1 270 SKAGGQSMGKKPRARIKAFANIGSDPALMLTGPVDVTEKLLKRSGMSLSDIDLFELNEAFAAVVLRYMQ 338
                                               ********************************************************************* PP

                                 TIGR01930 323 elgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               +++ +d++++NvnGGAiA+GHPlGa+Ga+i+ t+l+eL++r+ + +l+tlC+g G+G+A+++e
  lcl|NCBI__GCF_000023185.1:WP_012755967.1 339 AFD-IDHDRINVNGGAIAMGHPLGATGAMILGTVLDELERRDLNTALVTLCIGAGMGTATVIE 400
                                               ***.88*******************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (402 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.08
//
[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