Alignments for a candidate for fadA in Ruegeria conchae TW15

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Ruegeria conchae TW15

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_010437861.1 G7G_RS0102215 3-oxoadipyl-CoA thiolase

Query= metacyc::MONOMER-3207
         (400 letters)



>NCBI__GCF_000192475.1:WP_010437861.1
          Length = 400

 Score =  535 bits (1379), Expect = e-157
 Identities = 269/399 (67%), Positives = 318/399 (79%), Gaps = 1/399 (0%)

Query: 3   DVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQAGE 62
           D FICDA RTPIGR+GG+L+ VR DDLAA+P+ ALI  NP V W  +D+V +G ANQAGE
Sbjct: 2   DAFICDAQRTPIGRYGGSLSQVRTDDLAAIPIAALIARNPQVDWTGIDDVIYGDANQAGE 61

Query: 63  DNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMSR 122
            NRNVARMA LLAGLP  +PG T+NRLCASGMDA+G A RAI +G+ ++AIAGGVESMSR
Sbjct: 62  SNRNVARMAALLAGLPVDVPGTTINRLCASGMDAVGMAARAIRAGDYDMAIAGGVESMSR 121

Query: 123 APFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRADQD 182
           APFVM KA S +SR   + DTTIGWRF+NP MK ++G+DSMPETADNVA+ Y ++R+DQD
Sbjct: 122 APFVMPKATSAFSRANSVYDTTIGWRFVNPKMKQEFGIDSMPETADNVAEAYGINRSDQD 181

Query: 183 AFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGE-TIVERDEHLRPETTLEALTKLKPVN 241
           AFA RSQ + AAA   G F EEI PV I  +KG+  +V+ DEH RP TT E L+ LK +N
Sbjct: 182 AFAERSQARWAAAHQTGVFREEITPVTIPQRKGDPVVVDTDEHPRPGTTAEKLSGLKGIN 241

Query: 242 GPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVPA 301
           G DKTVTAGNASGVNDGAAA+++A+  A  K+ LTP ARV+GM+  GV PRVMGIGPVPA
Sbjct: 242 GLDKTVTAGNASGVNDGAAAILMANESAAAKNDLTPIARVVGMSVAGVEPRVMGIGPVPA 301

Query: 302 VRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGMS 361
            RK+  R G+++   DVIELNEAFASQGLA LRELGV DDAP VNPNGGAIA+GHPLGMS
Sbjct: 302 SRKVLARAGLSIDQMDVIELNEAFASQGLATLRELGVPDDAPHVNPNGGAIAIGHPLGMS 361

Query: 362 GARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           GARLV+TA +QL ++GGR  L TMCVGVGQG AL +ERV
Sbjct: 362 GARLVMTAAYQLRRTGGRYALCTMCVGVGQGAALILERV 400


Lambda     K      H
   0.318    0.134    0.383 

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: 520
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: 400
Length of database: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
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_010437861.1 G7G_RS0102215 (3-oxoadipyl-CoA thiolase)
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.3678285.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-137  445.0   2.3   1.3e-137  444.8   2.3    1.0  1  NCBI__GCF_000192475.1:WP_010437861.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000192475.1:WP_010437861.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  444.8   2.3  1.3e-137  1.3e-137       1     385 []       5     398 ..       5     398 .. 0.94

  Alignments for each domain:
  == domain 1  score: 444.8 bits;  conditional E-value: 1.3e-137
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaalaaglp 71 
                                           i da Rtpig++ggsl++++ +dL+a  i +l++r+ ++d   id+vi+G + qage   n+aR+aal aglp
  NCBI__GCF_000192475.1:WP_010437861.1   5 ICDAQRTPIGRYGGSLSQVRTDDLAAIPIAALIARNpQVDWTGIDDVIYGDANQAGESnRNVARMAALLAGLP 77 
                                           789*******99**********************************************9************** PP

                             TIGR01930  72 esvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl 144
                                            +vp++t+nr+CaSg++Av +aa++i+aG++d+++aGGvEsmSr+p+++++++   s+  ++++++d+++  +
  NCBI__GCF_000192475.1:WP_010437861.1  78 VDVPGTTINRLCASGMDAVGMAARAIRAGDYDMAIAGGVESMSRAPFVMPKAT---SAFSRANSVYDTTI--G 145
                                           ************************************************99973...33334455555333..1 PP

                             TIGR01930 145 ..........vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...kkv 204
                                                     +    sm etA+n+a+ ygi+R++qD++a rS+ + a+A++ g f +ei+pv+++++   ++v
  NCBI__GCF_000192475.1:WP_010437861.1 146 wrfvnpkmkqEFGIDSMPETADNVAEAYGINRSDQDAFAERSQARWAAAHQTGVFREEITPVTIPQRkgdPVV 218
                                           3467888886556679*************************************************999**9** PP

                             TIGR01930 205 vskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagv 277
                                           v++De++rp+tt+ekL++Lk +    +  tvtAgN+s++nDGAaa+l+++e++a++ +ltp+ar+v+++vagv
  NCBI__GCF_000192475.1:WP_010437861.1 219 VDTDEHPRPGTTAEKLSGLKGINGL-DK-TVTAGNASGVNDGAAAILMANESAAAKNDLTPIARVVGMSVAGV 289
                                           **********************985.66.7******************************************* PP

                             TIGR01930 278 dpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsld.lekvNvnGGAiAlGHPlGasG 349
                                           +p++mg+gpvpA++k+L++aglsi+++d++E+nEAFA+q la  +elg  d    vN nGGAiA+GHPlG+sG
  NCBI__GCF_000192475.1:WP_010437861.1 290 EPRVMGIGPVPASRKVLARAGLSIDQMDVIELNEAFASQGLATLRELGVPDdAPHVNPNGGAIAIGHPLGMSG 362
                                           ************************************************855689******************* PP

                             TIGR01930 350 arivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                           ar+v+t +++L++ g++y+l t+Cvg GqGaA+ile
  NCBI__GCF_000192475.1:WP_010437861.1 363 ARLVMTAAYQLRRTGGRYALCTMCVGVGQGAALILE 398
                                           **********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (400 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.44
//
[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 2024 update 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